Naruto: Johto Journeys

by KitsuneDragon

Naruto is a young trainer who wishes to become a Pokemon Master. With his trusty Cyndaquil by his side can he overcome the challenges he will face and make his dream a reality? Pairing: NarutoxHinata and SasukexSakura.

35. Chapter 35:The Fallen God

Naruto: Johto Journeys

Chapter 35: The Fallen God

"Pokemon" Normal speech

'Pokemon' Normal thoughts

"Pokemon" Pokemon that can talk

"Pokemon" Flashbacks

"Pokemon" Pokedex speech

Disclaimer: I don't own Naruto and I don't own Pokemon. I do however, own this laptop and this story and NONE OF YOU CAN HAVE IT!

---

Illex Forest

"Mah Mah, Naru-chan, that's so mean. I'm Minato Namikaze...I am...your father."

Silence filled the air to all that heard this. The thunder claps, the sound of pounding rain and howling winds were all but white noise as the five young trainers stared at Minato.

"WHAT?!"

Everyone stared at the blonde man with shock written across their young faces. Kushina sighed, resting her hands on her hips and shaking her head.

"Damn it Minato-kun, I told you not to suddenly drop the bomb on Naru-chan, but do you listen to me? Noooooo." A vein pulsed on her forehead. "I know you are a genius, but sometimes you can just be a complete idiot!"

"M-M-Minato Namikaze..." Sakura stuttered.

"Is the dobe's..." Sasuke's eye twitched in disbelief.

"Father?" Hinata and Akatsuchi could have caught Yanma in their mouths with how much they were gaping.

The group turned to the blonde. Naruto bent his head low and his body shook lightly. Kushina and Minato looked at their son in worry. They looked at each other before Minato stepped forward and bent down on one knee.

"Naru-chan, listen to me. I know it's a lot to take in, I mean I haven't been in your life for the past twelve years and I completely understand that you're very confused...but I'm here now. I'm here for you, Naru-chan." Minato spread his arms out and gave his son the fatherly smile he reserved for Naruto and Naruto alone.

"You..." Naruto walked towards the former Pokemon Champion slowly, his friends parting before him so he could get a clear path towards him. "You...You...Y-You..." Naruto continued to repeat the pronoun as he got closer and closer to his father. Kushina watched with interest at the scene before her, but the worry was clear in her gray-green eyes.

'Naru-chan...'

---

"Otou-sama, they're distracted. Attack them!" Wallace exclaimed.

"I would...but that man down there...is Minato Namikaze and the woman beside him, Kushina Uzumaki. Both of them are high level trainers, a former Champion and the second runner-up for the Pokemon League during their early years as trainers." Nagato turned to see Lugia and Ho-oh still laying on the ground, trying to catch their breath from having received brutal Sky Attacks to the chest. "Not to mention Lugia and Ho-oh are still recovering and they have the Legendary Birds on their side. It would be a fool's errand to attack them even with them distracted."

Wallace, Sapphire and Ruby looked at their father before turning to the older blonde and his red haired wife. The three executives of ROOT gulped audibly. Just what kind of monsters were those two trainers that they put even their father in a stationary position.

---

Naruto came to a stop as he stood in front of Minato. His body shook, his fists clenched tightly as he stood before the man who came down from the heavens on flying birds of legend and proclaimed to be his father. The younger blonde's head snapped upwards and Minato sucked in a breath when he saw just how similar his son was to him.

'You really are my son...aren't you, Naru-chan.' However, Minato frowned deeply when he noticed the cerulean orbs that were not much different from his own. Naruto looked at his father and was filled with a mixture of emotions. First there was shock, then surprise, then sadness, followed by happiness and complete confusion. All in rapid succession. However, his brain reduced the hormones and signals going throughout his body before focusing on a single emotion.

Rage.

His blue eyes flashed with complete and utter anger, his lips curling into a fierce snarl. Hell, he even managed a bestial growl. And then...he did something completely unpredictable.

He punched Minato Namikaze in the throat.

Everyone's eyes bugged out of their head in shock, while the former Champion's eyes bugged out of his head due to the sudden blow to his trachea. The man coughed violently as he felt as if his throat was about to collapse, clutching the C-shaped cartilage.

While everyone else was busy staring at the scene in complete shock, Kushina, being the loving wife she was decided to do what all wives would do in her position. She laughed. Loudly.

"Oh-Oh-Oh...Oh my...by Arceus hahahahaha, did you...did you see your face?!" Kushina held her stomach. "I swear that was priceless! Way to pull an Uzumaki on your old man, Naru-chan! Oh if only I could have recorded that!"

'Did Naruto just punch a Pokemon Champion in his throat?!' His friends and their Pokemon watched the teenage blonde with chibified shocked looks on their faces. Their skin was completely white and they looked as if they were a part of the artistic piece known as 'The Scream' given to how they clutched the sides of their heads.

"N-Naru..." Minato coughed once more before being grabbed violently by the collar of his cloak and pulled directly to face the angry eyes of his son.

"You...YOU IDIOTIC SON OF A BITCH!"

'He got his mother's anger.' Minato thought as he gulped audibly. 'This is not good.'

"That gulp was not nearly as audible as I'd like it to be you bastard!" Naruto exclaimed. "What the hell is wrong with you?! You come down from the sky riding a Legendary Bird, save our lives and sudden proclaim you're my father?! Then you think that just because you're the Champion that everything is fine and dandy and that I'll hug you and we can kick ass together as father and son?!"

Minato sweatdropped as he looked at his son with a nervous look. That was actually an entirely accurate explanation of how he expected the situation of his return to his son to go. Tis a shame it didn't. Minato coughed once more before giving his son a sheepish grin.

"Y-Yeah...but you gotta admit, your father being the Champion and riding down from the heavens of a Legendary Pokemon did look pretty badass, right?"

"Oh hell yeah that was fucking awesome!" Naruto exclaimed as he suddenly did a complete one-eighty, his blue eyes sparkling with childish awe. "And the fact that my father is the Champion is just completely mind blowing, I mean I can finally rub it in the teme's face that my parents are now entirely way more badass than his because I mean, you and Kaa-chan are way better than his parents since you guys technically beat them when you guys were in the Pokemon League tournament during your early days! I mean you are THE Champion, the one who dethroned Izuna and A. Not to mention you pretty much brought an end to ROOT thirty years ago by yourself and then..."

The sound of a record scratching to a halt filled Naruto's head as he suddenly snapped his head up. A look of realization flashed across his face before he faced Minato once more with rage filled eyes.

"OI! Don't try to distract me from this!" Minato cursed in his mind at how his son caught on to his plan. "But then again we have to save the world from being destroyed by the time stream imploding in on itself so you're escaping for now, you bastard...but this is not over." Minato glanced to the side, but Naruto pointed his finger harshly against his father's chest. "Look at me when I'm talking to you old man."

"Yes sir." Minato replied meekly.

"When we're done saving the world from certain doom, you, me and Kaa-chan are going to sit down and have a looooong talk. You're not getting out this Tou-chan!" Naruto growled out. "Not on your life."

He let go of Minato and dusted his hands off. The older man bowed down on his hands and knees to his son. "Yes, Naru-chan."

"Good." Naruto then turned to his mother. "I think your scolding me when I was younger really paid off in the long run."

"That's my boy." Kushina and Naruto bore matching foxy grins. The group of young trainers, Pokemon and the ROOT members all stared at the three members of the Uzumaki-Namikaze family with extremely large sweatdrops and looks of complete and utter disbelief.

'What the hell just happened?!'

Nagato shook his head to get rid of the unnecessary thoughts and feelings he was currently experiencing.

"Enough!" Nagato's voice carried itself over the battlefield and thus the previous air of seriousness returned with a vengeance. Everyone turned to face Nagato and his children. "Minato Namikaze, you and my traitorous cousin may be strong, but you are in no way capable of taking down the might of two deities of our world!"

As he said this, Lugia and Ho-oh rose to their feet. They released their deafening cries to the heavens before flapping their monstrous wings, taking to the skies once more.

"Cousins?" Naruto asked.

Kushina nodded. "It's a shame you had to find out this way, Naruto, but the truth is...Nagato's full name is Nagato Uzumaki."

Everyone's eyes widened at that, even those of Nagato's children.

"What?!" Naruto exclaimed. "So you mean, Wallace, Ruby and Sapphire are..."

"That's right. Those three are relatives of yours."

"Is this true, Otou-sama?" Ruby asked. Nagato nodded his head.

"It is, but do not let that deter you, Ruby. Family or not, these people stand in the way of bringing back your mother, from bringing back Konan-chan. The time draws near, in approximately thirty minutes, the time to open the gate into the space-time continuum will be upon us." The head of ROOT said as he glanced down at the Pokegear he took out of his pocket. Putting away the device, Nagato pointed at the group of adversaries.

"LUGIA! HO-OH!" The Rainbow and Diving Pokemon readied themselves for battle once more. "ATTACK!"

"Zapdos and Pikachu, use Thunder!" Minato commanded. The two Electric-type Pokemon nodded at the former Champion's command. Minato's partner Pokemon hopped onto the back of the thunder bird before they both took to the skies. Zapdos unleashed a mighty cry and the cumulonimbus clouds crackled with electrical energy.

"GAYOOO!"

"PIIIIKAAAAACHUUUUUUU!"

A massive thunderbolt shot forth from Pikachu's body as it clutched the electric sacs on its cheeks while an even larger streak of lightning fell from the heavens per Zapdos's will. The two electrical attacks flew towards the Lord of the Sky and Beast of the Sea. Lugia quickly folded its wings and its eyes shone with the trademark blue that came with the use of telekinetic abilities. A massive orb of psychic energy formed around it and the Rainbow Pokemon.

A massive explosion occurred in the skies which was akin to a crack of thunder. When the light from the twin Thunder attacks died down, it revealed Lugia and Ho-oh to be hovering proudly in the air. Lugia looked to the three Legendary Birds. As the Legendary Beasts were to Ho-oh, the Legendary Birds were the subordinates of Lugia. The dual-type Legendary looked to the three birds of Kanto and nodded its head, to which they nodded back.

Articuno swooped down and Kushina leaped onto the Pokemon's back. The Ice Pokemon narrowed its crimson eyes at the two deities before unleashed a battle cry.

"Aritcuno, Blizzard!" Kushina ordered. The Ice/Flying-type's body seemed to shine as the light from the lightning in the sky reflected off of its wings before it flapped the two appendages roughly, unleashed powerful gusts of freezing wind. The ice particles that were said to make up its body swirled into the winds and the Blizzard attack rushed towards Lugia. However, the Ice-type move was quickly interrupted by Nagato's command.

"Ho-oh, Flamethrower attack." The violet eyed man spoke calmly. Ho-oh took to the stand and unleashed a massive Flamethrower attack. The powerful stream of violet flame washed over the weaker move like river water over stone. Articuno's eyes widened at how easily it had been overpowered, but Kushina quickly reacted to defend her Pokemon.

"Moltres, Kyuubi, absorb the fire!" The Ninetails leaped onto Moltres's back and the Flame Pokemon shot into the air and dove right into the stream of violet fire. Despite the fact that it could absorb the flames, the initial impact against Ho-oh's Flamethrower did damage Moltres somewhat. The Legendary Bird powered through and used its natural ability to absorb fire while Kyuubi utilized its Flash Fire ability.

"Now follow up with a Shadow Ball on Lugia and Moltres use Sky Attack on Ho-oh!"

The stream of violet fire vanished from view as the two Fire-types finished their job. Moltres unleashed a cry as its body glowed with golden light before speeding towards Ho-oh. Once they got close enough, Kyuubi leaped off of Moltres's back and then open its maw, a blob of shadow and dark energy charging within. Once the energy was charged to its maximum, the blob of shadow was shot forth.

"NINE!" Kyuubi cried out as the Shadow Ball zoomed towards Lugia and the streak of gold that was Moltres aimed its sharp beak at Ho-oh's body.

"Ancientpower." Nagato stated coldly. Lugia and Ho-oh had their bodies covered with a powerful aura of silvery white energy and the earth beneath them began to quake and shudder. Large pieces of rock hovered in front of their bodies, some with trees of the Illex Forest still attached to them. Kyuubi's Shadow Ball shattered one stone and Moltres had to power down and stop using Sky Attack as both Legendary Pokemon bombarded it with massive stones.

Moltres turned back and caught the falling Fox Pokemon just as one of Lugia's rocks was about to crash into it. Moltres continued to go into a dodging frenzy, Kyuubi doing what it could by hitting a few with Flamethrower to deflect some of the relatively smaller projectiles. Articuno unleashed a massive burst of cold from its body, freezing a large amount of the rocks with a Blizzard attack before a Thunderbolt from Pikachu and Zapdos shattered the ice covered projectiles.

"Look out!" Kushina called out to the five airborne Pokemon as the remainder of massive pieces of earth shot towards them. Ho-oh unleashed a burst of flame that covered the rocks in fire and Lugia gave the projectiles a telekinetic push to boost their speed. The three Legendary Birds and two regular Pokemon could only brace for impact.

"Not on my watch!" Minato's voice rang out. As he said that, three loud cries echoed through the air before a large wall of spiny tree roots appeared in front of the airborne Pokemon. The burning rocks crashed into the wall with devastating force, causing the thick roots to bend backwards, but they managed to remain sturdy.

"What the..." Nagato looked to Minato and his eyes widened when he saw the blue eyed Champion standing with the three Kanto starter Pokemon.

"Nice job, Venusaur!"

"Saur." The Seed Pokemon nodded stiffly, sweating lightly as it took a lot of effort to stop those giant rocks and create such a large amount of tree roots with Frenzy Plant. However, as the burning rocks began to fall, the Frenzy Plant roots wrapped themselves around them and tossed back up into the air. The Legendary Birds took their passengers and

"Now Hydro Cannon and Blast Burn!" Minato ordered. Charizard and Blastoise nodded their heads. Charizard took in a deep inhalation of air while Blastoise readied its cannons. Twin blasts of pressurized water and a massive tongue of white flame shot through the air and pushed the Ancientpower attack right back at Lugia and Ho-oh.

"Lugia use Hydro Pump! Ho-oh, Flamthrower!" A powerful burst of pressurized water and violet-white fire rushed towards the burning spheroids and a the five attacks collided in midair. A massive explosion seemed to rock the heavens themselves as pieces of burning rock mixed in with embers and water flew every which way.

"Scatter the smoke, Lugia!" Nagato ordered. Lugia unleashed its song-like cry as it flapped its wings. The black smoke was reduced to nothing and a tornado formed in the process. The massive tempest dug a trench in the earth as it raced towards the enemy Pokemon and trainers, but Kushina and Minato would have none of it.

"Articuno, use Ice Beam!"

"Charizard use Air Slash!"

Articuno opened its beak and a sphere of glowing ice blue energy formed. Articuno then let the energy loose and jagged bolts of icy energy raced through the air and impacted with the wind circulation system. In a matter of seconds, the Ice Pokemon froze the entire tornado and a beautiful ice sculpture was created. However, no one had enough time to gaze at the structure before Minato's Charizard roared and flapped its wings, making slicing motions with them. Two crescents of pure air launched themselves towards the tornado and those that watched could only stare in complete awe as the massive tornado was sliced apart. Lugia and Ho-oh could only stare in completely shock as the thick slabs of ice fell to the ground, creating small clouds of dirt and dust when they impacted with the ground.

"Take advantage of their shock and take 'em down!" Minato and Kushina exclaimed.

"THUNDER ATTACK!"

Zapdos soared above the two larger Pokemon before unleashed its cry alongside the Electric Mouse that was its passenger. The clouds above crackled with blue electricity and Pikachu charged a massive amount of electrical energy in its body as it squeezed its cheeks. The necessary amounts of electricity took mere milliseconds to accumulate and with that, the two Electric-types attacked.

A pair of massive bolts of blue electricity fell from the heavens as if Arceus itself had cast divine judgement on the two other godly Pokemon. Ho-oh and Lugia could only stare in shock before the two Thunder attacks crashed down on their bodies. Their cries echoed through the air as thousands of volts of electricity coursed through their frames. When the lightning died down, smoke rose from their bodies before they fell back to earth, shaking it when they made impact. Sparks of voltage flickered around their form, their muscles twitching as a result.

Super Effective indeed.

The younger trainers stared in awe. Akatsuchi then scooted a little closer to his blonde friend and leaned down to his ear.

"Naruto...your parents are awesome." The Hiker said. Naruto could only nod dumbly in response. It wasn't vanity, but not many trainers could up against ROOT executives and come out like he and his friends could, so they all knew that they were good trainers, great in fact. But Kushina and Minato...those two were on a whole other level. Kushina had taught Naruto everything he knew about Pokemon battling and Minato had dethroned a Champion...

"Awesome yes, but those two are monsters. It makes you wonder how you would turn out in a few more years, Naruto." Sakura added. Everyone looked at Naruto as the pink haired girl said, but he paid them no heed as he was too busy trying to wrap his head around the fact that his parents were kicking Legendary Pokemon ass.

Nagato stared in shock as he saw his two most valued weapons had once again fallen to the ground. He then looked around him as he saw what remained of his guard army. Due to the Pokemon used by those brats, his grunt army had been reduced from hundreds to mere tens and none of the offending Pokemon had been taken down yet. Every single one of them stood, albeit they were still injured greatly.

"No! Not when I'm so close!" Nagato growled with rage, clutching his red hair so tightly that it seemed as if he were about to wrench them free of his skull. The leader of ROOT turned to his children and pointed an accusing finger at Minato and Kushina.

"Kill them!"

He pointed to every person and Pokemon that he saw as an enemy. "Kill them all!"

The three young admins nodded as they and their father took out their Pokemon. Six Champion class Pokemon and eighteen Gym Leader class Pokemon stood before the others.

Minato and Kushina cursed through gritted teeth. They were strong, but they weren't invincible and they weren't stupid either. Nagato had power that rivaled Izuna's and with so many powerful Pokemon on his side, they wouldn't last the remaining twenty-five minutes they had left before the head of ROOT would catch Celebi for his own. Lugia and Ho-oh were already beginning to climb back to their feet and no doubt the enemy Pokemon would work to act as shields to protect the two deity Pokemon.

"Kushina."

"Yeah?"

"I know I don't deserve it, but I need to take Naruto away from the battlefield."

"What?!" She exclaimed. "Minato-kun, I don't know if you realize this, but we're in a war right now! With Legendary Pokemon in the mix!"

"I know, but the Legendary Birds and Beasts aren't going to be enough to take them down. Those two there..." Minato pointed at the two gargantuan Legendary Pokemon. "...one rules over the Legendary Birds and the other practically created the Legendary Beasts. It'll be a harsh battle, but in the end the six of them aren't going to be enough to take down Ho-oh and Lugia. I need to take Naruto with me to get the ace in the hole I think we might have."

"What ace in the hole?"

"It's difficult to explain, but it's one of the reasons why I wasn't able to come home during the past twelve years."

"Wha-"

"Please Kushina." Minato's blue eyes stared into his wife's gray-green ones with a pleading look. He needed her to understand and trust him for the meantime. "I promise, when this is all over, I will answer everything you question, but please."

Kushina bit her lip, but nodded her head.

"Zapdos, Articuno, Moltres, keep it up and distract them!" Kushina ordered her three Legendary Pokemon. "Kyuubi, hop off and provide cover fire!"

"Pikachu, Venusaur, Blastoise, provide ground support! Charizard, stick with Articuno and provide defense against any Fire-type moves in the air!"

The Pokemon did as their trainers instructed and went on with the battle they were currently undergoing. Minato and Kushina nodded in satisfaction at the scene before they turned to the younger trainers.

"Which one of you kids has some healing items?" Kushina asked. All of them nodded their heads to the red haired woman before she gestured to the downed forms of Raikou, Entei and Suicune.

"You two..." Kushina pointed at Hinata and Sakura. "...heal the Legendary Beasts." Hinata and Sakura didn't need to ask why and simply did as they were told. They raced over to the Legendary Beasts and began to take out every single health restoring item they had and worked to help Suicune, Raikou and Entei recover.

"Sasuke and other kid!"

'Other kid?' Akatsuchi frowned at his title.

"I need you to work fast. Your Pokemon have been fighting without commands and they're running low on steam! Take charge and defeat the remainder of the grunt army so as to protect the girls and their Pokemon while they work to heal Raikou, Entei and Suicune!"

Sasuke and Akatsuchi nodded before running off to do as they were told.

"Naruto." Naruto looked his mother as she called to him.

"Yeah, Kaa-chan?"

"I know this doesn't look good, but your father has a secret ace in the hole and he needs you to go with him. Gather up your Pokemon. Minato-kun will heal them for you before you two head out."

"What?! No way! I'm not abandoning you nor my friends!"

"Naruto!" Kushina's voice was stern and it forced Naruto to shut up. "I know you don't want to leave us and I know you don't like Minato-kun right now, but he is your father. He's a brilliant man overall and his plans have always had a tendency to pull through in the end. Whatever plan he has, you are a key factor in it so please, listen to me and do what Minato-kun tells you to do. Promise me?"

Naruto stared at his mother in shock. She was never this paranoid, but then again that could be due to the war going on, but still he never knew her to lose her cool to this degree. The younger blonde nodded his head before holding out his Poke Balls.

"Everyone, return!" Beams of red light shot forth and the six Pokemon were sucked into their Poke Balls. Kushina gave her son a loving smile before kissing him on the forehead.

"Remember your promise." She said and with that, she got up to help the and returned his Pokemon to them. Naruto ran up to his father as the older blonde gave the command for his Charizard to knock down Ruby's with an Air Slash. As he watched the enemy Flame Pokemon collide with Wallace's Blastoise, he looked to see his son standing by him.

"You ready to go?"

"Yeah, but..."

"No time, give me your Pokemon." Minato ordered. Naruto did as the former Champion said and held out his Poke Balls before Minato reached into his pocket and pulled out a small device which had a green neon light attached to it. Kind of like what the machines in the Pokemon Centre had. Minato pressed a trigger on the device and Naruto's Poke Balls were all bathed in the comforting green glow of the machine.

"What was that?" He asked as his father pocketed the device.

"Portable healing machine. Issued to Pokemon Champions only." He stated. The older blue eyed blonde then cursed as he heard the Rainbow Pokemon and Diving Pokemon release their respective cries.

Lugia and Ho-oh slowly rose back to their feet. Ho-oh screeched and the sun's light tore through the cumulonimbus clouds, coating it and Lugia with its gentle rays. By the power of the Lord of the Sky, the sun healed their wounds and brought them back to fighting strength. It was as if they hadn't been struck by a Thunder attack at all.

Nagato laughed like a mad man, his violet eyes holding a great deal of insanity, or something close to it.

"Do you see this?!" Nagato exclaimed. "My Pokemon, my children's Pokemon, they are some of the best Pokemon this world has to offer! The gods of the region stand behind me and offer me their strength! And soon, the temporal powers of the universe will be at my fingertips! You cannot stop me! Not even you, Minato Namikaze and Kushina Uzumaki! None of you!"

"Shit!" Minato exclaimed loudly. "Charizard!"

The Flame Pokemon unleashed a powerful Flamethrower and Air Slash combo which effectively created a cover explosion for it before it took off towards Minato and Naruto. Minato grabbed his son's arm and then leaped into the air just as Charizard dove down. Landing atop the Flame Pokemon, Minato adjusted himself and his atop on the Fire/Flying-type's back before it flapped its large wings and took off through the skies.

"Where are they going?!" Sakura asked as she took notice of Minato and Naruto leaving on the roaring draconian Pokemon.

"Minato-kun and Naru-chan have a plan to help us beat Ho-oh and Lugia, but Minato-kun said he can only take Naruto. He couldn't explain it in detail, but you'll just have to trust in my husband and son." Kushina replied as she continued to bark orders to the Legendary Birds, Kyuubi and her husband's Pokemon. The others could only nod and put their faith in the father-son duo.

'Be careful, Naruto-kun.' Hinata thought.

---

"Where are we going?!" Naruto yelled. Minato didn't reply as he just kept staring straight ahead, Charizard's wings flapping dangerously fast. The younger blonde grabbed his father by the shoulder and shook him harshly.

"Oi! Old man!"

"We're heading for the Kanto region." Minato's calm voice replied to his son's outburst. The former Champion turned around to face his son with a serious look on his face.

"Kanto?" Naruto tilted his head in confusion. "Why are we going to Kanto? What's this plan of yours? Old man, if I'm going to trust you like Kaa-chan wants me to, you need to answer me."

"I will, Naru-chan." The older blonde said. "Like I told Kushina-chan, there's a potential ace in the hole that we can use to help us even the odds against Lugia and Ho-oh, not to mention it could help completely overpower Nagato himself."

"Elaborate." Naruto folded his arms over his chest and Minato could only chuckle at the posture.

"You look just like your mother when you make that face." He laughed. The younger blonde blushed lightly in embarrassment before undoing his crossed arms. "Alright, well Naruto first off I'm going to have to go into a very long story which should take about as long as it would take to get to our destination. Charizard knows where to go so I don't have to tell him anything, in case you were wondering."

"Listen to me, Naruto I will explain everything when we get to where we need to. I promise you that, but right now I need to focus on having Charizard move as fast as he can go."

Naruto growled at his father's reply, but nodded in compliance. "Fine, but I'm gonna kick your ass if you're not gonna tell me."

His father merely laughed.

---

Kanto Region

Flying past Mt. Silver, the Pokemon League and Viridian City, the two airborne blondes had seen from their draconian steed that ROOT had not been joking around when they said they would try to take over the entirety of the joint regions. Pokemon battles raged right and left, flames burned brightly due to the attacks of explosion making attacks. Either that or some deadly Fire-type moves.

The Uchiha Police worked alongside their Pokemon and the Kanto Gym Leaders. Viridian City had been one of the most titanic ones as Minato and Naruto had managed to catch a mere glimpse of a Gyarados tearing apart the city with its Hyper Beam only to be One-Hit K.O-ed with a swift attack from a Rhydon's Rock Blast.

"Seems A hasn't lost his touch." Minato smirked as he watched the Rhydon vanish into the distance.

"A? You mean your rival?"

"Yup. Most stubborn bastard I've ever come across, but he was no doubt the best. He had beaten Izuna before me and so he was Champion for a while before I came to the Indigo Plateau. He held the position for only a day and I'd snatched it away from him. I was ruthless back in the day, but fighting a criminal organization can do that to a guy."

"I know what you mean." Naruto muttered.

In a matter of minutes, Charizard's fast moving form had cut around Pewter City and bypassed Mt. Moon. The father-son duo found themselves gazing at the war zone Cerulean City had become. Numerous amounts of slithering Gyarados fought against each other, or rather it was numerous amounts of Gyarados against one other. And that one other was kicking some serious ass with how it easily maneuvered around multiple Hyper Beam attacks and countered with its own.

"Zabuza's doing well it seems." Minato commented.

"Old man, just how strong are these Kanto Gym Leaders?"

"Just as strong as Johto, but Gym Leaders can't be put on a scale against one another. Some are stronger than others and some are weaker than others. It's just the way the world works. Now come on." Minato pointed down below where a cave entrance was visible across the river that flowed by the Nugget Bridge. Charizard landed in front of the cave entrance and bent down for its passengers to hop off.

As they did so, Minato and Charizard took point while Naruto followed behind his father. Looking around the relatively dark cave complex, Naruto unconsciously reached out with hand and gripped his father's cloak. The older blonde blinked in confusion before turning back to see his allegedly fearless son glancing around the depths of the cave.

"This place is different from other caves." Naruto commented. Minato nodded his head, but didn't comment on his son's action nor on how right the boy truly was. After a while of navigating through the cave complex, Naruto looked to his father and gripped the man's cloak tighter to get his attention.

"Ok then. Well tell your story, Old man." Naruto motioned for his father to talk. "You promised once we reached our destination you'd talk and unless there's something connected to this place then I know that this where we need to be. Now talk."

Minato nodded his head and continued to lead his son through the cave complex, the light of Charizard's tail flame casting long shadows on the floors and the walls.

"Alright, Naru-chan. I will, but in order for you to understand why we came to this place I need to start from the beginning. Many years ago, while I was still a trainer and still undergoing the Gym Leader challenge, it had been almost six months and I was already on my way to earning my seventh badge from Fugaku Uchiha Senior, the Gym Leader before the current Fugaku Uchiha Junior, that is, your friend Sasuke's grandfather."

"Seventh badge in six months? Damn Old man, you weren't a Champion for nothin' it seems."

"Damn right." Minato ruffled his son's hair causing the younger blonde to scowl.

"And how do you know Sasuke-teme?"

"Your mother and I talked on the way to the Illex Forest before we swooped in to save you and your friends." Minato explained. "Anyway, before I went to take on Fugaku Sr., I had decided to do some exploring, or rather I was forced to. The door to the Cinnabar Island gym was locked for some reason and a few members of the management staff said that the key had been left behind when Fugaku Sr. had went to do some training in the Pokemon Mansion. Personally, I think it was because of his old age. Fugaku Sr. was never all that right in the head when I met him for the gym battle."

"What's the Pokemon Mansion?" Naruto asked.

"It was once a proud and beautiful building back in the day I'm sure, but when I was there, it was old and burned. Apparently a great fire had occurred in the mansion, burning nearly everything inside the mansion. Due to being uninhabitable for people, Pokemon such as Grimer, Zubat, Golbat, Growlithe and the ocassional Vulpix and Ninetails had made their home in the mansion." The former Champion answered. "Anyway, while I was exploring the mansion to help look for the lost key to the Cinnabar Island gym, I came across a few journals. They were mostly burned, but there were a few entries in each journal that were readable."

"What did they say?"

"Apparently the journals were research journals because they talked about some rather scientific stuff. One entry spoke of a place called Guyana where they had managed to find what they thought was a new species of Pokemon and decided to call it Mew."

"Mew?"

"Yes, Mew. Another journal entry spoke of how upon finding the Mew, they chased after it, but it vanished before they could even get close to it. But when they looked over the area where the Mew had vanished, they came across the remains of one of the Pokemon making the scientists realize that Mew was actually a very ancient Pokemon, possibly the first Pokemon in existence." Naruto's eyes widened at that revelation. "Taking the DNA of the Mew remains, the scientists then began to do even more extensive research into the Pokemon that was Mew and eventually they began seeking...outside help...for their research."

"Outside help?" Naruto asked. Minato nodded.

"Yes and that outside help came in the form of ROOT. Danzo was as ambitious and mad as he had been back in those days as well because the journals went on to explain that upon receiving funding and resources from ROOT, Danzo had wanted the scientists to do the unthinkable. He had them compensate for the help with their research by having them undergo an operation to clone the Mew using the DNA they had with them."

"Clone a Pokemon? But how is that even..."

"Possible?" Minato finished his own son's question. "Genetic engineering, gene splicing, anything is possible if you put your mind to it Naru-chan and ROOT had the scientists clone Mew, but with some modifications. They worked to make the clone faster, stronger, more powerful than any other Pokemon in the known world in order for the clone to surpass its genetic predecessor. The Pokemon was a monster and it showed no mercy when it came to taking down its opponents."

Naruto stared at his father as he noticed the fearful look in the older blonde's cerulean orbs. "Y-You met it...didn't you?"

"Mewtwo." The former Champion uttered. "Mewtwo is the name of that abomination. The power of a god that could rival even that of Legendary Pokemon such as the ones you've met, possibly capable of exceeding that power, Mewtwo was like a fallen god forced to live its life amongst us mortals. The power of Mewtwo was too great for ROOT to handle and the Pokemon League Association had gotten tipped off on ROOT's workings into the cloning process. Mewtwo had been created already however and so Mewtwo did what it was created to do. It became a weapon, but of its own volition and tore apart everything around it. The Pokemon League Association had sent in Izuna and the Elite Four to handle the problem when it was shown that Mewtwo was too powerful for their executive members as well as the ROOT members to handle. The Pokemon League and ROOT had undergone a momentary truce to seal away Mewtwo because they knew it was too powerful to kill."

"Mewtwo's in the Kanto region...isn't it? That's why we're here." Naruto said this as more of a statement than a question. His father nodded in confirmation.

"Yes, right here in this very cave complex. The Cerulean Cave to be exact. A deep network of caverns that tunnel beneath the Kanto region near to Cerulean City."

"Old man...how do you know all of this? I mean, sure you read some journals, but the Pokemon League Association stuff, how..."

"When I became Champion, I became the strongest trainer in the entirety of Kanto and Johto. It was after you were born and before I had...left...you and Kushina-chan alone and the Pokemon League Association thought that since I had the power to overthrow Izuna, the man who helped seal away Mewtwo, that I would have the power to potentially tame it, kill it if the need should arise. They told me everything. The Pokemon League Association told me about ROOT, the scientists, the cloning operation, everything. When I received that information, I was then tasked with the responsibility as a Champion to take down the monster that was Mewtwo."

Minato released a hollow laugh that made Naruto shudder. He looked past the older blonde and saw Charizard, who had been listening in on the conversation, begin to shudder in fear. Seeing the power of his father's Pokemon, Naruto knew Charizard to be one the man's most powerful Pokemon so if something had the Flame Pokemon this spooked then just what was this Mewtwo?

"I went to Cerulean Cave and I didn't even know what I was getting into, I mean, I fought Izuna Uchiha and won so I thought it was something along those lines of strength, but Mewtwo far exceeded that. Naru-chan, Mewtwo was the hardest battle I had ever encountered. Even as a wild Pokemon it had the highest level of attack, speed, defense and intelligence I've ever come across. Even if it was a Psychic-type, Mewtwo was on a whole other level that placed it into the category of being a Legendary Pokemon. I was actually forced to flee because once that thing took down my Snorlax, with only a few Psychic attacks mind you, I knew I had to get out of there. I was traumatized by the incident."

Naruto could only stare in awe at his father. The former Champion was not lying and not playing around with the words that came from his lips and the younger blonde held a new found respect for the man.

"So what's the plan?" Naruto asked.

"You and I...we're going to fight Mewtwo and capture it." Minato said. Naruto's eyes widened at that.

"But...But you just said that it was a monster. Not even you had been able to beat it, what makes you think that having me around could help?! I'm a kid!"

"A child you may be, but you're my child." Minato said as he placed a hand on Naruto's head. "That and the fact that you are the only human capable of catching Mewtwo. I'm just going to be there to help."

"Me? How can I help catch a monster Pokemon?" Naruto asked.

"Because you have the ability to communicate with Pokemon."

"Huh?"

"Every since you were a baby, even after I left, I saw how you acted around Pokemon. You got along so well with them it made many older trainers jealous because of how Pokemon immediately took a liking to you and so as you grew up, Kushina-chan told me of how that you had the capability to talk to your Pokemon."

"Well so can others."

"Yeah, but you can talk to any Pokemon. A trainer can only talk with a Pokemon that they have a true bond with, their partner Pokemon. Me and Pikachu, Kushina-chan and Kyuubi, Izuna and his Charizard, we're in a close enough bond that we can understand them, but you, Naru-chan...you have the gift of speech. The gift to talk to any and all Pokemon."

"But I can't talk to Legendary Pokemon. I tried with Raikou, but it..."

"Raikou and the others, those Pokemon can only be heard unless they want to be. Mewtwo is not one of the true Legendary Pokemon and so there is the possibility for it to be able to be talked to. You can listen to it, you can hear its heart and voice and if you're anything like your mother and I, then you've got the silver tongue to go with everything you have. You can convince Mewtwo to be our ally and capture it."

"But what if it doesn't work? Mewtwo is not going to let me sit on a couch and talk about our problems like some shrink."

"I know that, Naru-chan, but that's why you're only to be able to talk to it when we've caught it."

"And how exactly are we going to catch it?" Naruto asked. Minato smirked and reached into his cloak's chest pocket before taking out a small sphere.

'A Poke Ball?' Naruto thought, but his eyes widened when he saw the Poke Ball wasn't just any ordinary Poke Ball. Minato clicked the centre button and the ball expanded to its full size. It was noticeably larger than an Ultra Ball. Its top half was coloured with a deep purple and had two pink circles on either side of it. Just above the centre button, a white 'M' was emblazoned on it.

"This is the Master Ball." Minato started before Naruto could even ask. "A special Poke Ball constructed by Silph Co. When I helped stopped ROOT thirty years ago in Saffron City, the president in Saffron City gave it to me in thanks. I never had a chance to use it until now. And if you're about to ask what's so special about it, the answer is that it can never fail. Any Pokemon you want to catch, you use the Master Ball and it will shake three times no matter if the Pokemon is at full strength or completely weakened."

Naruto's eyes brightened with childish awe. "So cool." He muttered. "And you're sure we can catch Mewtwo with this."

"Indestructible and can catch any Pokemon without fail? As long as we don't die trying, I'm sure as hell that we can catch Mewtwo with this bad boy." Minato shrunk the Master Ball back down to size before putting it back in his cloak pocket. Naruto grinned it at his father.

"Well then...let's catch us a Mewtwo." Minato sent a matching toothy grin back to the younger blonde.

"That's the spirit."

Minato then chose to pick up the pace. Twenty-five minutes had been left when they left Illex Forest. It took Charizard five minutes to reach the Cerulean Cave and so they had thirteen minutes left before Celebi could be used by Nagato which meant they had fifteen minutes at the most to do what they came here to do. Minato used his experience navigating through the Cerulean Cave and in no more than three minutes did it take the former Champion to help lead his son to the lowest area of the Cerulean Cave.

Minato and Naruto took out their Lapras and Quagsire respectively before crossing the waters that flowed through the area. Soon, they came to the island that lay in the centre of the Cerulean Cave's lake. They climbed up onto the shore and Lapras and Quagsire stayed beside their trainers as they observed the single figure that rested atop the large island.

"Quaaag." The Mud Fish Pokemon shuddered.

"It's okay Quagsire. I know you're feeling afraid, but you gotta be strong for the team, okay? We got a lot of lives riding on this mission being a success." Naruto patted his Water/Ground-type's head causing the Pokemon to feel a sense of calm at its trainers words. The Mud Fish Pokemon nodded. Minato and his Transport Pokemon smiled at the scene before they turned back to their objective.

Naruto took a deep breath and he and Quagsire walked up and stood a suitable distance away from the cloned Pokemon.

It was a bipedal, humanoid creature with some feline features. It was primarily gray with a long, purple tail. On top of its head were two short, blunt horns. A tube extended from the back of its skull to the top of its spine, bypassing its neck. It had a defined chest and shoulders, which resembled a breastplate. The three digits on each hand and foot had spherical tips. Its tail was thick at the base, but thinned out before ending in a small bulb. The Pokemon sat in a cross-legged position, hovering over the ground with its eyes closed as if it were meditating, but it remain that way for long.

Its eyes snapped open and a pulse of pure power raced out from its body, the bright blue glow completely encompassing its eyes. Naruto and Quagsire stared in awe at the power of the Genetic Pokemon while Minato and Lapras narrowed their eyes as the memories of their previous battle with the clone of Mew came to the surface.

The blue glow died down within the Genetic Pokemon's eyes and cold violet irises stared at the opponents that stood before it. Mewtwo's body continued to hover before it stretched out its legs, touching down softly on the cold stone of its island of solitude.

"Mewtwo?" Naruto took a step towards the clone of Mew, but that was a mistake on his part. As soon as he did that, the powerful Psychic-type regained the powerful blue glow in its eyes, immediately seeing Naruto as a threat. It opened its mouth and a loud cry echoed through the Cerulean Cave and a powerful wave of psychic energy tore across the island.

"Lapras, use Blizzard!"

"Laaaaaaa!" The Water/Ice-type unleashed a powerful flurry from its mouth and a massive wall of ice stood in front of Naruto and Quagsire. The force with which the telekinetic blast crashed into the ice wall was practically cataclysmic. The Blizzard wall cracked and broke apart at some areas and Naruto and Quagsire looked at each other and then to Minato.

"YOU WANT TO CATCH THAT?!" Naruto exclaimed.

"Focus, Naru-chan!" Minato alerted his son. As he said that, Naruto and Quagsire saw was looked like a large blade of pure telekinetic energy sliced through the ice wall. The ice wall split into two parts as Mewtwo's Psycho Cut finished carving its way through the defensive ice barrier and then Mewtwo held out a hand, the ice wall pieces covered in an aura of blue.

Raising its hand, the pieces of ice all hovered in the air and cast large shadows over Naruto and Quagsire. Sure Psychic-type Pokemon could levitate objects with ease, but depending on the size of the object it required great amounts of focus to do so. Large objects such that these two pieces of Lapras's Blizzard wall would have made even an Alakazam sweat, but Mewtwo did it without even a hint of unease.

Mewtwo then flicked its wrist and the ice blocks shot forth at high speeds.

"Lapras, Psychic!"

"Quagsire, use Mud Bomb!"

A burst of telekinetic force and a massive orb of liquefied earth shot forth from the two Pokemon and collided with the oncoming ice blocks. Mud Bomb shattered one ice block into mere shards while Lapras's Psychic sent the other careening off-course and splashing into the surrounding waters.

"Use Blizzard on the ground to create an ice path then slide on it to get close and use Mud Bomb!" Quagsire let loose a burst of freezing winds and Mewtwo raised a non-existent eyebrow as a road of ice was created. Quagsire's ran and then slid on its belly, using its tail to turn as it moved on the ice road. Mewtwo growled in annoyance as Quagsire's rapid movements began to confuse it, but before it could act, Lapras fired off an Ice Beam.

The Genetic Pokemon's eyes narrowed at the Ice-type move and held out its hands. A blue sphere of energy charged in front of it, humming with power, before it was launched. The Aura Sphere tore through the air and collided with the Ice Beam causing a small explosion in midair, but that was when Quagsire attacked and used a Mud Bomb.

Mewtwo turned and generated a blade of telekinetic energy and sliced through the Mud Bomb with its Psycho Cut and an arc of telekinetic energy continued to soar towards Quagsire. However, Quagsire used its ice road to avoid the attack and the energy blade sliced through the ice road, the thick rock of the island and the water of the lake before it caused a devastating explosion against the far-off wall of the cave.

Minato took out two other Poke Balls while Naruto took out his remaining five.

"Snorlax, Charizard!"

"Typhlosion, Amphoros, Pidgeot, Heracross and Dragonite, you're up!"

The seven Pokemon stood at the ready, their eyes glaring at Mewtwo. Quagsire raced back to its fellow Pokemon's sides as they all stared down Mewtwo. The Genetic Pokemon stared back at them and unleashed a flare of energy and killing intent. The others flinched a bit.

'Did it just...smirk?' Naruto thought. Ignoring the thought, Naruto shook his head before pointing at Mewtwo. "Quagsire and Typhlosion use Earthquake!"

The Mud Fish and Volcano Pokemon nodded and raced up to the front. Typhlosion reared back a forelimb while Quagsire turned around so its back was facing the Genetic Pokemon and raised its tail. Both appendages slammed into the ground and the seismic waves raced out from the point of impact. Mewtwo stumbled as the force of the earth racked its body.

"Amphoros Thunderbolt!" Naruto commanded. The Light Pokemon sent forth a powerful bolt of lightning, but Mewtwo's glowing blue eyes shone brighter and the thunderbolt was stopped cold before being redirected towards the party of nine. "Quagsire, take the hit!"

The Water/Ground-type took the shot and due to its Ground-type characteristic, the Thunderbolt did it no harm.

"Snorlax use Shadow Ball!" Minato ordered. "Lapras, follow up with a Surf attack!" Lapras did as it was told and quickly returned to the massive lake and zoomed around the island so it was on Mewtwo's right. With a loud cry, the waters of the lake churned and then a massive wave of water raced towards the Genetic Pokemon while Snorlax lazily opened its jaws and then fired off a blob of shadow once it had finished charging.

Mewtwo roared, leaping into the air before slamming its equivalent of a fist down on the ground. The earth shuddered and shook as a mighty blast of telekinetic energy raced out of Mewtwo's body. The Surf attack crashed into the dome of energy and was split apart while the Shadow Ball was completely overwhelmed and destroyed in a violent explosion of energy and dark matter.

Mewtwo then held out a hand and Lapras's eyes widened as it was suddenly caught in Mewtwo's psychic hold.

"Dragonite use Dragon Rush!" Dragonite's body was coated in a blue aura that then turned into the image of a mighty winged serpent. Dragonite roared as it raced towards Mewtwo. The Genetic Pokemon released a cry of defiance and hurled Lapras towards Dragonite, but the Dragon Pokemon performed a barrel roll and avoided the Transport Pokemon before it crashed into the ground.

Dragonite took on another boost of speed and the sound barrier shattered with a deafening boom. Mewtwo crossed its arms as Dragonite rammed into it. Mewtwo skidded backwards from the force of the blow, gritting its teeth to bite back the cry of pain.

"Now Snorlax, use Earthquake to disorient it and then follow up with Shadow Ball!" Snorlax took the front lines and then slammed its feet on the ground sending a rush of seismic waves at the Genetic Pokemon, but the clone of Mew had been accustomed to seeing this maneuver. The cons of using a predictable move like Earthquake.

Mewtwo hovered in the air before zooming forth.

"Dragonite, Pidgeot, intercept!"

The two winged Pokemon soared towards Mewtwo. Pidgeot's wings shone like silver while Dragonite glowed with its draconian shaped, blue aura. Dragon Rush and Steel Wing slammed into the Legendary Pokemon's body sending it soaring through the air.

"Now Charizard, hold it still! Snorlax fire that Shadow Ball!" Charizard did as it was told and raced towards the airborne Psychic-type, but the powerful telekinetic recovered in midair just as Snorlax fired the Shadow Ball. The blob of Shadow zoomed towards them as Charizard placed Mewtwo in a choke hold, but the clone of Mew elbowed the Flame Pokemon in the stomach before slamming its head backwards, hitting Charizard in the snout.

Charizard released a roar of pain, clutching its muzzle before Mewtwo's tail wrapped around its throat. Mewtwo then swung Charizard around and tossed it towards the Shadow Ball, firing off a Psychic attack for an increase in the time it took for Pokemon and Ghost-type attack to collide. The Fire/Flying-type unleashed a roar of pain before falling to the ground, but Typhlosion and Amphoros managed to catch it.

Mewtwo then took part in its original plan and took off towards Snorlax. Heracross went to attack, its claws encompassed with dark energy as it went in for a Night Slash attack. Mewtwo countered it, gripping the clawed appendage before it make contact and slammed a knee into the Bug/Fighting-type's stomach. The dual type Pokemon's eyes widened as blood and spittle flew from its mouth before it was tossed aside like a ragdoll and Mewtwo finally made it to its target, Snorlax.

The tank of a Pokemon bellowed loudly and it fired off numerous Shadow Ball attacks. Mewtwo barrel rolled to avoid the first and then shot skyward to avoid the second. Dragonite had gone in to attack with a Thunder attack from behind, but Mewtwo loop-de-looped over the Flying/Normal-type just as Snorlax sent out its third Shadow Ball. Mewtwo smirked before allowing gravity to take its hold on it and the attack collided with the Thunder attack creating a smokescreen to blind the Dragon Pokemon.

A fourth Shadow Ball raced towards Mewtwo, but the Genetic Pokemon formed a massive spoon entirely out of telekinetic energy and swung it like sword to initiate its Psycho Cut attack. The powerful move tore through the Shadow Ball and slammed into Snorlax with tremendous force, sending the Sleeping Pokemon skidding backwards.

"Don't give up! Use Crunch!" Snorlax opened its jaws to clamp down on Mewtwo as it neared its form, but Mewtwo spun around and lashed out with a brutal roundhouse kick that had Snorlax stumbling before a tail strike to the face had it stumbling back even more. Snorlax dug its claws into the ground to remain stable and Mewtwo moved it with an energy spoon to deliver a close range Psycho Cut.

"Lapras knock it aside with Psychic to Snorlax an opening! Snorlax you follow up with Giga Impact!" A telekinetic blast from the Transport Pokemon stopped Mewtwo from making contact with the Sleeping Pokemon and was sent off to the side as Snorlax batted it away with a clawed paw. Mewtwo rolled on the ground to prevent any major damage from the fall, but quickly rose to its feet as Snorlax charged forward at a speed unheard of for the heavy weight Pokemon.

A cloud of spiraling violet energy outlined with orange surrounded the massive Pokemon as it stampeded towards Mewtwo. The clone of Mew's eyes widened at the incoming giant and quickly reacted. Minato stared with wide eyes as it saw Mewtwo run up to Snorlax and then, utilizing what could be described as one of the greatest acts of "using your opponent's momentum against them", tossed the Sleeping Pokemon over its head. Snorlax's jaws were agape in shock as earth met sky and it was upside down in the air.

Mewtwo then met the massive giant in the midair and drew back an arm. Aura swirled to life and formed a compact sphere before the Aura Sphere was jammed into Snorlax's body. Snorlax unleashed a roar of agony as the attack drilled into its body and sent it flying through through numerous boulders and stalagmites. Just as it came to a stop, the Pokemon made by science had already appeared in the giant Pokemon's face, hand drawn back with a spiraling ball of aura hovering in its palm.

With a roar, Mewtwo slammed the Aura Sphere against Snorlax's body. The smell of burning flesh filled the damp cave as the attack drilled into Snorlax's thick body before the explosive force of the Aura Sphere sent the heavy weight Pokemon tumbling along the ground. Snorlax didn't even have time to recover before Mewtwo dove down from above and slammed another Aura Sphere, this one against Snorlax's face. A flash of blue marked the explosion and Snorlax lay on the ground with a bloody face and stomach, covered in burns from the super effective strike.

Mewtwo then raised the Sleeping Pokemon into the air and looked to see Minato. The violet eyed Pokemon snarled at the one that had disturbed its period of isolation those many years ago and proceeded to hurl Snorlax at him. Minato's eyes widened and quickly took out Snorlax's Poke Ball and returned it in midair. However, as Snorlax vanished into red energy, the Psychic-type moved in close to Minato.

The former Champion's eyes widened before gripping Mewtwo's arms at the wrist as they tried to make impact with him. The powerful Pokemon gritted its teeth in anger, but its glowing blue eyes narrowed in annoyance when it saw the playful smirk on Minato's face.

"Quagsire, use Hydro Pump!" A blast of pressurized water nailed Mewtwo in the back causing both it and Minato to fly through the air, however, Charizard appeared to snatch Minato away from the enemy Pokemon before spinning and slamming its tail against the Psychic-type.

"Fire Blast now!" Minato commanded. A ball of yellow-orange flame sped through the air before it exploded outwards to take on the shape of a five pointed star. The blast of yellow-orange flame slammed into Mewtwo causing it to slam into one of the large boulders that decorated the Cerulean Cave's island of solitude. Mewtwo fell to the ground as it did so before unleashing a roar of anguish and lifted the boulder with ease and sent it flying through the air with a telekinetic push.

"Lapras freeze that rock with Ice Beam!" The rock continued to fly through the air, but Lapras's Ice Beam covered it in ice and thus made it brittle.

"Amphoros shatter that rock with Iron Tail and then join with Dragonite for a joint Thunder attack!"

"Amphoros!" The Light Pokemon's tail shone like silver before it leaped at its target and spun around. The momentum carried itself across and the iron hard rear appendage shattered the boulder of ice like it was made of glass. Amphoros was then caught in the air by Dragonite and the two glowed with electrical energy, sending off dual bolts of golden lightning.

Mewtwo raised up a few more boulders, hurling one to take the shot. The boulder exploded into dust and pebbles before a second one was sent at the two airborne Pokemon, slamming into them harshly. Dragonite and Amphoros released cries of pain as they were sent tumbling through the air and landing on the ground in a tangle of limbs.

Mewtwo unleashed a cry as it summoned forth its energy spoon and swung it in an arc to generate its Psycho Cut, however, the attack was sliced apart by Heracross's Night Slash.

"Now Close Combat!" Naruto commanded. The Bug/Fighting-type then rushed forward and delivered a furious set of blows as it utilized Close Combat. Heracross delivered a a swift elbow strike to the stomach followed by a series of rapid jabs to the stomach.

"Now finish it with Megahorn!"

"HERA!" The Fighting Pokemon slammed an elbow to Mewtwo's jaw before delivering a flying knee to the chin causing the powerful Pokemon's lower jaw to meet the upper one with a resounding clack. Heracross landed on the ground before spinning around, its horn glowing with a pale green light. The glowing horn was brought up in a swift arc, but the trainer and Pokemon were caught by surprise when Mewtwo's tail wrapped itself around the sharp horn, holding it back from making contact.

Mewtwo looked to the younger of the two blondes, its glowing eyes seeming to stare into his soul. The son of a Champion then felt as if something were entering his mind and his eyes widened when heard a chuckle.

'You amuse me.'

'What the hell?' His thought was brought to a stop when Heracross was slammed into the ground, the glow from Megahorn vanishing.

"Heracross, sweep its legs out from under it and go into a Close Combat again! Pidgeot attack from behind while its distracted with Fly!"

Heracross spun around on the ground, lashing out with its legs, but Mewtwo hovered over the attack before Heracross rotated its body and then performed a cat spring, leaping back onto its feet and went into the string of attacks that made up Close Combat.

However, the weaponized Pokemon dodged every single strike before grabbing Heracross's left wrist when it went to strike at its throat. Mewtwo got behind Heracross, twisting the arm in the process and lengthened out the limb, locking it at the joint before lashing out with its large tail. The force of the strike on the exoskeleton covered joint was great and the sound of bone snapping echoed through the air. Mewtwo then tossed Heracross at Pidgeot when the Bird Pokemon dove down from above.

The Bird Pokemon squawked in surprise as it collided with the Fighting Pokemon, injuring its friend with the super effective attack that was Fly. But Mewtwo didn't stop there as it flew up at Pidgeot and Heracross, kicking the Fighting Pokemon away and then grabbed Pidgeot by its wings as it stamped down the Flying/Normal-type's back. The force of the stamp worked in tandem with Mewtwo's pulling up Pidgeot's wings and the Bird Pokemon unleashed a shriek of pain as its wings were torn from their sockets with a sickening pop. Mewtwo then flipped in midair and crashed its tail down on Pidgeot sending it back to the ground.

Naruto gritted his teeth as he returned Heracross and Pidgeot back to their balls as they had fallen unconscious.

Mewtwo then soared towards Naruto himself and summoned forth its energy spoon. Naruto's eyes widened as the Pokemon neared him, but he was tackled to the ground by his father while the Genetic Pokemon was suddenly tackled by Typhlosion.

"Naru-chan!" Minato looked at his fearful son who was shaking lightly.

"Huh?"

"Are you okay?" Minato asked. Naruto looked over himself before looking to his father.

"You...You saved me?"

"Of course I did." Minato said as he pulled Naruto to his feet. "Truthfully I would relish the moment and use this event to make you love me like I am your father, but now's not the time for sappy moments. Typhlosion needs some commands."

Naruto nodded his head and slapped his hands against his cheeks, ridding himself of the fear of nearly being bifurcated by a homicidal Pokemon before looking to see Typhlosion and Mewtwo rolling on the ground. However, Mewtwo gained the upperhand and straddled Typhlosion and unleashed a furious barrage of rage fueld punches to the face.

Blood flew from Typhlosion's lips with each strike before a hammer blow nailed it across the cheek and one of Typhlosion's teeth was removed from its gym with a few drops of blood. Mewtwo then grabbed Typhlosion by the neck and began to push down with physical strength and Psychic. Typhlosion gasped as it was being choked to death, the Psychic attack not helping at all as it was being pushed down into the earth. A crater formed beneath Typhlosion as Mewtwo applied more and more force.

But the telekinetic user was sent flying through the air when Lapras attack it with a Psychic attack. Mewtwo tumbled through the air and tried to regain its sense of balance only for it to be hit with a stream of fire from Charizard. An Air Slash followed after sending it to the ground, but Charizard zoomed around the falling Pokemon and opened it maw, a vortex of energy swirling to life.

"DRAGON PULSE!"

"Quagsire, follow up with Hydro Pump!"

The violet-gray vortex slammed into Mewtwo and the Psychic-type was sent back into the air just in time to receive a powerful blast of water to the back.

"Dragonite and Amphoros use Thunder!"

"Lapras help out with a Thunderbolt!"

Minato and Naruto's Pokemon unleashed their respective attacks of golden voltage, but Mewtwo quickly erected a Barrier attack and defended itself against the oncoming onslaught. While it hadn't used Barrier earlier due to believing its strength to be greater than that of the its nine opponents, which it did, but due to the teamwork displayed by father and son, Mewtwo's need to cover all its bases started to come about.

Mewtwo unleashed a burst of telekinetic force and flew towards Lapras. The Transport Pokemon's eyes widened as it slammed into. Mewtwo pushed Lapras along the water's surface at breakneck speeds, nearly making it a literal expression too when it grabbed Lapras by the head and, in a great feat of physical strength, hurled the Water/Ice-type through the air. A Psycho Cut attack left a large bloody gash on its underside just as it impacted with the ground.

Minato was forced to recall his second Pokemon just as Amphoros and Dragonite went to intercept. Dragonite and Mewtwo flew towards each other, but Dragonite suddenly spiraled above Mewtwo and the Light Pokemon riding atop its back, dropped down onto Mewtwo's surprised form. Mewtwo acted quickly and grabbed Amphoros before unleashing a powerful Psychic attack that slammed the Light Pokemon into a far-off wall.

"AMPHOROS!" Naruto called out to his Pokemon before gritting his teeth. "Dragonite attack with Dragon Rush and Thunder!"

Mewtwo and Dragonite rushed at each other, but Mewtwo quickly lowered its flying form to go beneath Dragonite's aura covered one and lashed out with a powerful Psycho Cut. Dragonite was sent soaring through the air, but the Dragon Pokemon recovered quickly before unleashing a massive lightning bolt from between its antennae.

Mewtwo cried out in pain as the electrcity coursed through its body.

"Dragonite follow up with Outrage!" Dragonite nodded and then its eyes glowed with red light before unleashing a loud cry. Red-violet flames rushed out of its body and slammed into Mewtwo. Wave after wave of the powerful Dragon-type attack collided with Mewtwo sending it careening through the air.

Minato and Naruto turned to each other and nodded. Now was their chance.

"Typhlosion, catch Mewtwo and ground it before going into a roll! Put your weight behind the roll and throw Mewtwo into the air!" The Volcano Pokemon miraculously gained the upper hand as it did as it was told. Having then gripped Mewtwo by the shoulders and hurled it overhead, Naruto made the call.

"Shoot it down with Flamethrower!"

"Increase the fire's intensity with Air Slash, Charizard!"

Charizard swung its wings as Typhlosion unleashed a burst of red hot flames. The flames combined with the arcs of pressurized air sent powerful arcs of flame at Mewtwo. The Genetic Pokemon growled and summoned forth its psychic spoon and used Psycho Cut to cleave apart the flaming arcs.

"Use Eruption!" Naruto ordered. Typhlosion nodded and raised up both forelimbs and planted them into the ground. The island began to shake as Typhlosion channeled massive amounts of fire from its body into the earth and then the earth burst apart as large amounts of fire and molten rock shot up from the centre of the island. Burning rock and a large streak of fire erected a pillar that then curled and lashed out at Mewtwo.

The Psychic-type Pokemon unleashed a deafening cry of pain as its body was swept away by the current of fire, slamming it into the ground and continued to push it along the ground, through some of the boulders that lay scattered on the island. It didn't help that Mewtwo was also being pelted by the pieces of burning rock that came with the formation of the Eruption attack.

Mewtwo came to a stop as it was returned to the centre of its island of solitude, but that was the two Fire-types acted once more.

"CHARIZARD..."

"TYPHLOSION..."

"FINISH IT WITH BLAST BURN!"

Typhlosion and Charizard's weakened forms had their Blaze abilities burning brighter than before. With eyes glowing with fiery crimson light, Typhlosion dropped onto all fours while Charizard inhaled deeply. Flames of pure white then rushed forth from the Volcano Pokemon's neck flames while Charizard breathed out a massive torrent of its own white fire from its jaws.

Mewtwo's eyes widened and quickly summoned forth a Barrier. The ultimate Fire-type move struck with devastating force and sent the Barrier encased Pokemon skidding along the large island, a molten trench marking its path. That's when Mewtwo began to hear the cracks, its eyes widening as it watched its psychic barrier beginning to break apart.

"GOOOO!" Minato and Naruto exclaimed. With a final roar of effort, both Fire-types put as much energy as they could into the Blast Burn attacks and Mewtwo watched as its Barrier was shattered. The attack pushed against the powerful clone as its already burned form was burned even more, being pushed through the air before slamming into the waters of the surrounding lake with a massive explosion.

Steam rose into the air as Mewtwo was pushed into the lake. The Pokemon made by science sunk beneath the waves of the lake as the now boiling area of water began to die down. Naruto and Minato looked to their panting starter Pokemon before grinning widely.

"We beat...Mewtwo." Minato chuckled.

"Yeah, we did. I'll just send Quagsire down below to get its unconscious body and then it's back to saving the day."

However, the celebratory mood was cut short when the waters began to bubble. Naruto and Minato's eyes widened along with the eyes of their tired Pokemon as a massive tower of water formed with explosion of psychic energy. Within the tower of water, a pair of violet eyes shrouded by the blue glow of psychic energy pierced through it. The water then fell away to reveal Mewtwo's form.

Minato and Naruto couldn't help but hiss as they looked at it body. Burns covered its entire body and the skin that once covered its left arm and pectoral, part of its stomach, the right side of its face, part of its tail and the entirety of its right leg had been burned away. The blood covered muscle tissue was visible for all to see, but the rage in its eyes was clear.

Mewtwo panted as it hovered above its island before standing in the centre of it. Mewtwo unleashed its cry, but then the cry died down as Mewtwo fell to its knees. Naruto then took the Master Ball from his father and the blonde man nodded and gestured for his son to go to the defeated Pokemon. Naruto ran up to the Genetic Pokemon before slowing down, standing before the burned Pokemon.

Having stood at a height of over six feet, the Genetic Pokemon's kneeling form was still able to look Naruto in the eyes. Violet eyes stared into sapphire ones before Mewtwo closed its eyes.

'Do it.'

"Huh?" Naruto tilted his head in confusion. His eyes widened as he recognized the deep voice. 'So you really did talk back there.' Naruto looked to his father and saw that the man hadn't even reacted which meant that Mewtwo was selectively directing its thoughts to him alone. A few seconds passed as Naruto continued to stare at the Psychic-type.

Mewtwo's head snapped in his direction with surprise and anger.

'What are you waiting for?! You came here for me, didn't you?! Every time someone comes into here they aim to kill me! That's all they've ever tried to do for the past thirty years, but now you've defeated me!' Mewtwo glanced down at the ground with gritted teeth. 'Finish me! Deal the killing blow and then you humans will have what all always wanted, a destroyed weapon!'

Naruto's eyes widened as he heard Mewtwo's telepathic voice. Now he wasn't at all surprised by the fact that the clone of Mew could talk, even if it was via telepathy. It was the fact that Mewtwo now had tears in its eyes.

"Mewtwo...do you want to die?" Naruto asked.

"Naru-chan, what are you..." Minato was cut off when Naruto raised his hand, glaring at his father as he did so. Stay out of this. That was what the younger blonde was telling him. Minato nodded before stepping back to stand beside Charizard, but it, Typhlosion and Quagsire remained at the ready for just in case.

'I was created to be a weapon for the humans that created me. I surpassed every single expectation they had of me, but on the day they chose to set me free from that accursed tank they chose to subjugate me. That human called Danzo tried to make me his toy when he had spoken to me while I was in the tank, claiming that we would be equals as human and Pokemon standing together to represent an ideology of equality. But it was for naught. I snapped and I destroyed the laboratory I was made in. I was then chased into this place.' Mewtwo's burned visage gestured around the cave. 'My Fortress of Solitude as I like to call it, but even then...even when I just wanted nothing more than to be left alone, humans still kept coming after me. I was targeted to be killed and so...I returned the favour.'

"You killed people and their Pokemon?!"

'I did.' Mewtwo replied without any sort of shame or emotion. 'I had no purpose the day I failed to be the weapon Danzo so desired and I lost my individuality the day I was an enemy of the world. So I made it my purpose to protect the place I called home, to kill all that dared to intrude, but I see that I failed at that as well. I no longer have a purpose, human child. I no longer have anything to live for. I was created as a weapon and now...' Mewtwo's teary eyed form looked over the third degree burns. '...I have none. All that's left to do...is die.'

Naruto looked at the cloned Pokemon with a shocked expression before glancing at the Master Ball in his hands. He then set the the purple Poke Ball in front of Mewtwo causing the telepathic Pokemon to look at it with a confused expression.

"That's called a Poke Ball, Mewtwo...the Master Ball actually...and it is a capturing device used to be able to catch a single Pokemon without fail."

'So you would aim to subjugate me too?!' Mewtwo mentally shouted with anger flashing across its face. 'I still choose death!'

"You're right." Naruto admitted. "I did aim to subjugate you, to use you as a weapon and death does seem like a better alternative than to be a tool to someone else."

'So why won't you grant me that wish?!'

Naruto smiled at the enraged Pokemon. "Because I don't want you to be a weapon to me. I want you to be my comrade." Mewtwo's eyes widened in shock, silent at the sudden change in the boy's serious demeanour.

'C-Comrade?' The Genetic Pokemon thought the word as if it were a foreign concept.

"Yes, a comrade. Your plight, I realize, is one which many of us as Pokemon trainers tend to ignore. We catch Pokemon, we train them, make them battle for us, but yet there are times when we forget that Pokemon are individuals as well. We think that just because we are the trainers that there is a boundary line which places us humans at the top and the Pokemon at the bottom, but rather the possibility lies in the fact that it should be the other way around. You Pokemon are the gods of the world wielding powers that could never be thought possible. But the truth lies in that Pokemon and humans must live with equality."

'The Pokemon you fight with though, are they not your comrades? Do you subjugate them?'

"They are my comrades, the best Pokemon I could ever ask for to be my partners. But I do not subjugate them. They fight with me because they want to fight with me. They want to support me, care for me and be the best that they can be. We see each other as equals and your situation shows the reality that there are people out there that see otherwise." Naruto tapped the Master Ball lightly. "Mewtwo, I want to be your friend, your comrade in arms and your equal. I want to hear your story and be the one to help bring purpose back to you. My friends, my mother...they are all in the middle of a war that is going on across the entirety of the Kanto and Johto regions and currently, we are losing and we need your help."

'Losing? And you need...me?' Mewtwo asked. Naruto nodded.

"Yeah, we need you. Like I said, I want to be your friend and comrade in arms, Mewtwo. You have so much more to live for and you have the choice to be who you want to be, to live the life that you want to live and to be able to find your own purpose in life. I want to help you do that and so you begin your journey by helping my friends, my family and I to win this war." Naruto's eyes shone with determination and conviction. Mewtwo's telepathic abilities searched Naruto's emotions and mind and he found no alternate thoughts.

'You're telling the truth.' Naruto nodded at Mewtwo's statement. Mewtwo's violet eyes glanced between the Master Ball and Naruto before the clone of Mew closed them in thought. 'You practically sacrificed yourself to save the Pokemon and the people of this world. There are those who see us Pokemon as beneath them, but you and many others like you are willing to set aside your differences and reveal the true power that is held deep inside. I see now that the circumstances of one's birth are irrelevant and it is what you do with the gift of life that determines who you are.'

Naruto nodded in agreement. "So, what do you say? Ready to fight alongside us...partner?"

Mewtwo looked up and stared at Minato, Typhlosion, Charizad, Dragonite and Quagsire who seemed to be looking at him with expectant looks. The Genetic Pokemon chuckled in amusement.

'I wasn't lying when I said you amused me, human.' Raising a hand, the telekinesis user brought Naruto's Amphoros back from the crater in the wall and set it down beside Naruto. The blonde nodded in thanks as he returned the unconscious Electric-type to its ball.

"We're friends now." Naruto grinned. "You can call me Naruto."

Mewtwo nodded before tapping the Master Ball. The ball opened up and Mewtwo was sucked in inside and the Master Ball didn't event have to shake three times as it immediately registered Mewtwo as captured. Naruto's Pokedex beeped and reaching into his bag, he pulled out the orange Pokemon encyclopedia.

Mewtwo the Genetic Pokemon. A Psychic-type Pokemon. Because its battle abilities were raised to the ultimate level, it thinks only of defeating its foes. It usually remains motionless to conserve energy, so that it may unleash its full power in battle.

Naruto picked up the Master Ball and grinned toothily before turning to his father. The two returned their Pokemon to their balls before Minato fished out the portable Pokemon healing machine to heal the injured Pokemon. They attached their Poke Balls to their belts, but Naruto still held the Master Ball in his hands.

"ROOT dreamed of creating the world's most powerful Pokemon...and they succeeded." The younger blonde gripped the ball containing his newest capture. "Now let's head back and win this war."

(A/N: Yes, you read correctly. Naruto captured the most powerful genetically engineered Pokemon in the world. Naruto captured goddamn Mewtwo so the next chapter will be the end of the ROOT War Arc as I like to call it. Hope you all enjoyed reading this entirely new twist on the plot that I'm sure a lot of your did not expect to happen. Also to those of you that noticed, yes I did use lines from Pokemon the First Movie. Adjusted accordingly for Mewtwo's last bits of dialogue and Naruto's second to last piece of dialogue.

Hope you enjoyed the chapter. Review, Review, Review! Seriously, I really want to know what all of you guys think about this chapter.)

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Pokedex: Seen-186

Caught-117

Character Bio: Onoki

Eye Colour: Black

Hair Colour: Brown (in his prime), Gray (now)

About: When the modern day Kanto region created the Gym Leader challenge, Onoki was picked out of a number of candidates to become one of the eight and represent Pewter City as its Gym Leader. Onoki has held the position with great pride and has proven to be a worthy foe for any trainer, whether they are beginners or aces. He is extremely stubborn, quick to anger (especially when his age is brought up) and very prideful, never turning down from a fight. However, despite this he boasts an extremely tactical mind and is very calm in the face of battle. He lives for the fight and the adrenalin rush that comes with being a Pokemon trainer and is the main reason why he has held the Gym Leader position for Pewter for over seventy years. Though he constantly suffers from back pains and arthritis, the old man still does not wish to relinquish the position and will hold it until the day he dies. Or so he says.

Naruto's Team:

Typhlosion(Male)

Pidgeot(Male)

Heracross(Male)

Quagsire(Female)

Amphoros(Female)

Dragonite(Female)

Hinata's Team:

Espeon (Female)

Butterfree(Female)

Nidoqueen(Female)

Jumpluff(Female)

Lapras(Male)

Togekiss(Male)

Sasuke's Team:

Feraligatr(Male)

Sneasel(Male)

Gengar(Male)

Rapidash(Female)

Red Gyarados(Male)

Rhydon(Male)

Sakura's Team:

Meganium(Female)

Azumarill(Female)

Porygon2(No Gender)

Wigglytuff(Male)

Ninetails(Female)

Raichu/Pika(Male)

Akatsuchi's Team:

Golem(Male)

Steelix(Male)

Sudowoodo(Male)

Crobat(Female)