Author's Note: There seems to have been a little misunderstanding regarding my last author's note. This story is not the finale to this little "one-shot collection" I've been doing. There's going to be one more story after this one, and that story will probably be a two-parter as well. Until then, please enjoy the battle against Zygarde.

Disclaimer: I do not own Pokemon.


Project Z, Part 2

"So now Amber and Zwei have turned against Lysandre?" Mairin asked. "I can't tell if this is good or bad."

"One thing's for sure. This whole situation has gotten totally out of control!" Malva declared. "The whole city could be destroyed by Zwei and Zygarde's battle."

"So then what do we do?" Mairin asked.

"We need to get aboard Lysandre's ship and disable whatever he's using to control Zygarde," Malva answered.

"But how are we supposed to do that?" Alain asked.

Suddenly the three of them were enveloped in an almost blinding blue light. In moments the light faded, and Alain and the others found that they were on the platform of Lysandre's ship.

Lysandre quickly noticed their arrival. "So, it seems that our Ms. Amber is trying to enlist your help."

"Alain! It might make things easier for Zwei and myself if Lysandre's attention was divided!" Amber called. "I'll leave him to you!"

With that, Amber and Zwei flew further into the city away from the ship. Zygarde lumbered after them, crushing everything in its path.

"Lysandre… I don't understand any of this!" Alain told him. "You said that you wanted to create a better world!"

"And I am!" Lysandre declared. "I told you last night that destruction is often necessary for creation!"

"But this is going too far!" Alain responded. "All those lives that were just lost from Zygarde's attack… how can anything like that lead to a better world?"

"Do you feel the same way, Malva?" Lysandre asked.

"I do, Lysandre. If I had known that you had planned something like this… I had no idea you could be so heartless!" Malva told him as tears came to her eyes. "The idea that the man I… well, I guess now I see you for who you truly are. I can't be a part of this world you're trying to make."

"Then you can die with the rest of the world," Lysandre told her.

"Malva, you and Mairin take care to trying to shut down Lysandre's control device," Alain told her.

Malva nodded before wiping her eyes and turned to Mairin. "Let's go kid! We've got a job to do.

Mairin nodded, and the two of them ran off down the metal deck that attached to the platform and went all around that section of the ship.

"You know Alain, all this wouldn't have been possible without your help," Lysandre told him. "After all, you did help to charge the machine I'm using to control Zygarde."

"Then it is time that I atone for that," Alain spoke before tossing out a pokeball. "Go Charizard!"

Charizard burst out of the ball and roared at Lysandre.

"So be it," Lysandre responded as he produced his own pokeball. "Go Gyarados!"

Bursting out of Lysandre's thrown ball with a sparkling flash was a large red sea serpent resembling a Chinese dragon. It had green eyes and a large dark-red three-pointed crest on its forehead. Yellow spots traveled down the sides of its body, and it had a large gaping mouth with yellow lips and four small white fangs. Dark-red whiskers grew from the sides of its mouth and two large white fins on the sides of its head. Around its neck was a black metal collar containing a red, yellow and blue stone.

"Attack with Dark Pulse!" Lysandre commanded.

The stone in Gyarados's collar lit up, and suddenly it became enveloped in a blinding red light, which quickly faded to reveal Gyarados in a new form, and a multicolored DNA helix briefly shined above its head. The sea serpent's body had become bulkier and the crest on its forehead became much larger. The fins and whiskers on its head had become longer, and a long spike grew from the underside of its chin. The yellow spots that had originally run down the sides of the sea serpent's body had changed into raised dark-red scales. Growing from its back were two large white fins almost like the hood of a cobra.

As soon as it had finished transforming, Gyarados fired rings made of black energy from its mouth. The barrage struck Charizard in the chest, but the fire dragon was relatively unharmed.

"Charizard! Fight back with Thunder Punch!" Alain ordered.

Alain's keystone and Charizard's Mega Stone both lit up, and soon Charizard's body gave off a blinding flash of blue light in the shape of an X. In moments the light faded to reveal Charizard's mega form. The black dragon flew in close and struck Gyarados in the forehead with an electrified punch. Gyarados withstood the attack and roared at Charizard.

"Impressive as always!" Lysandre praised. "I think I'm going to enjoy this battle."


Amber and Zwei kept flying until they reached a large park near the center of the city. Zygarde was still fairly close behind them despite its slow pace. The duo landed in the park, after which Amber tossed out the pokeballs containing Mugen and Galatea. The chimera and mechanical Pokemon burst out and looked expectantly at Amber.

"So we're taking the battle here?" Zwei asked as she looked around the park.

"I thought this battlefield's large size would allow us to minimize the collateral damage," Amber explained.

"And they are to help as well?" Zwei asked, looking at Galatea and Mugen. "You're actually concerned that we can't defeat this opponent on our own?"

"We are not unbeatable, Zwei. Our encounter with Bianca taught us that," Amber pointed out as she touched her left shoulder, remembering her previous injury. "And Zygarde is said to be incredibly powerful. We'll need the added power of Mugen and Galatea to help bring it down."

'I'll do whatever I can to help, Ms. Amber,' Galatea's child-like voice spoke in Amber's head.

'Whatever opponent we're up against, I'll rip it to shreds myself!' Mugen's gruff voice declared.

"I admire your enthusiasm," Zwei told Mugen.

With a wave of Amber's hand, a pink disc flew out of her long coat towards Mugen. The port on the side of the chimera's head opened up and the disc flew into it. Afterwards the port closed up, and Mugen's eyes turned a light pink, as did the spikes on the back of his head crest and the membrane of his tailfin.

"I've loaded Mugen with the Fairy Memory, which should give him immunity from Zygarde's Dragon-Type attacks," Amber spoke. "Now here is the plan. Zwei and I will attack Zygarde from the air, while Mugen will attack him from the ground. Galatea, I will move you to a spot hidden from Zygarde's sight, where you can charge up and launch long-range attacks at it. Do you understand?"

'I'll do my best!' Galatea enthusiastically responded.

"Zwei and I will relay commands telepathically," Amber told them. "Now let us proceed!"

With another wave of Amber's hand, Galatea vanished with a flash of blue light and teleported to the branch of a tree. Soon after, Zygarde finally entered the park. Amber and Zwei took back off into the air. When they got high enough, Amber's keystone lit up along with Zwei's Mega Stone, and a second later Zwei's body gave off a blinding purple flash in the shape of a Y. The light soon faded to reveal Zwei in her Mega form.

The psychic feline then fired a beam of white electricity from between her hands that struck Zygarde in the chest, causing a large patch of ice to form where it struck. Down on the ground, Mugen fired a similar beam of energy from his jaws that struck Zygarde on the stomach and created another patch of ice there. Zygarde flexed its body and shattered the ice. It then turned its head to look down at Mugen and stomped its right foot into the ground. A wave of earth rose from the spot that Zygarde stomped on and came right towards Mugen.

Mugen jumped to the left and managed to avoid the attack, and then charged towards the beast at top speed. As the chimera came in close, his body began to crackle with pink electricity. Mugen then rammed into Zygarde's right shin with all his strength as his body gave off a brilliant pink flash. The impact caused Zygarde to stagger back to whole steps. Soon after from the trees, Galatea fired two beams of pink light from her eyes that struck Zygarde in the right shoulder, nearly causing the humanoid dragon to topple over.

Zwei fired another Ice Beam attack that struck Zygarde in the face, while at the same time Mugen fired an Ice Beam of his own that hit the beast's right waist. After a moment, Zygarde shattered the new ice that had formed on its body and fired a powerful blast of multicolored light from its chest up at Zwei and Amber. The duo quickly flew out of the beams path and managed to avoid getting hit. Zygarde then turned its attention back to Mugen and fired another blast from its chest. The beam hit Mugen and created a large glowing red Z on the ground around the chimera, but when the attack ended, Mugen was totally unharmed.

Before Zygarde could launch another attack, Zwei formed a ball of purple energy four times her size in front of herself and launched it at the dragon. Zygarde was hit in the chest by the attack, causing a massive explosion of light. When the light faded and the smoke cleared though, Zygarde seemed damaged but was still standing.

"Zygarde has much more stamina than we thought," Zwei and Amber spoke. "This is going to be a very long battle."


Mairin and Malva made it into what seemed to be some sort of engine room. At the very center was a gigantic scarlet crystal that bathed the giant room in a red light.

"So if we break that big crystal, will Lysandre lose control of Zygarde?" Mairin asked.

"There's only one way to find out," Malva answered as she took out a pokeball.

"Not so fast!" a voice spoke. Mairin and Malva saw Xerosic emerge from a dark corner of the room. "Did you not think I wouldn't know where you were going when I saw you run into the ship?"

"Well, you being here confirms we were right," Malva declared with a smirk. "That crystal really is how Lysandre is controlling Zygarde."

"That's right, and I can't let you destroy it!" Xerosic told her. "Not after all of the work I've put into it!"

"Then I guess we'll do this the hard way," Malva decided as she threw the pokeball she had just pulled out. "Go Delphox!"

Bursting out of the ball was a tall bipedal fox covered in thick dark-red fur resembling a robe. This robe of fur had orange flame-shaped patched near the beast's knees, and a large white patch on the stomach. Its head was covered mostly in yellow fur that grew down to cover its chest and shoulders, with giant tufts of red-orange fur like flames growing from its large ears. Thick dark-red fur covered its arms, and it had a tail covered in thick yellow fur. Its hands and feet were dark-grey, and in its right hand it carried a wooden stick like a wand with a flame burning at the top.

"Okay you pasty weirdo, let's rumble!" Malva spoke.


During this whole time, Alain and Lysandre's battle continued on the ship's platform. Charizard had taken quite a bit of damage from Gyarados's attacks, but showed no signs of going down any time soon. Gyarados on the other hand seemed to be on his last legs.

"Gyarados, attack with Dragon Tail!" Lysandre commanded.

"Dodge and use Thunder Punch once more!" Alain ordered.

Gyarados roared before flipping through the air as his tail began to glow with a green light. Charizard took off to the right to avoid the attack, causing Gyarados to strick the platform floor. The black dragon then got above the Gyarados and struck the sea serpent in the back of the head with another electrified punch. Gyarados collapsed and reverted back to his original form. Charizard returned to his original form and roared with triumph as he breathed a stream of flames into the air.

"Well done," Lysandre praised as he called Gyarados back to his ball. "But this changes nothing! Zygarde is still under my control! And not even the likes of Amber Drei and her Mewtwo can stop me!"


"Delphox! Finish off Xerosic's Crobat!" Malva commanded. "Mystical Fire!"

Delphox used its flaming want to draw a large circle of fire in front of itself. The fox mystic then breathed out a massive stream of flames through the ring at its opponent, a large purple bat with four green wings known as a Crobat. Crobat was completely enveloped by the flames. When the attack ended, the bat dropped to the ground unconscious. Xerosic turned even paler upon having his last Pokemon defeated.

"Now out of our way!" Malva told the scientist. "Use Psychic!"

Delphox's eyes glowed purple, and suddenly Xerosic and the unconscious Crobat glowed with a feint purple aura as they were suddenly lifted into the air and flung hard into the wall. The impact knocked Xerosic out cold.

"Whoa!" an impressed Mairin spoke. "I can't believe you finished him off so quickly."

"Well, I am a member of the Kalos Elite Four, you know," Malva reminded her. "Now Delphox! Use Psybeam to shatter that crystal!"

Delphox cried out as it fired beams of purple light from its eyes at the red crystal. The crystal cracked a bit upon being struck, and within a few seconds the beams caused a large chunk of the crystal to shatter apart. Soon after, the crystal stopped glowing and turned a dull grey.

"Looks like we were able to break it," Malva observed with a sigh of relief. "Now this madness will hopefully come to an end."


A yellow news chopper was in the sky above the park as Amber and her three Pokemon continued their battle against Zygarde. Suddenly Zygarde paused and the red parts of its body turned green. The markings on the wings hanging from its right shoulder had become blue, while the markings of the wings on its left shoulder turned red. Amber and the others paused, wondering if the battle was over. Suddenly Zygarde fired another beam from its chest up at Amber and Zwei. The duo managed to fly out of the way at the last second and avoided getting hit.

"Do you still fight because you're merely confused, or do you fight us because you consider us a threat to your ecosystem?" Amber and Zwei asked Zygarde together. "It wouldn't surprise us if you considered us a threat because we were not born by natural means. Either way it doesn't matter. This battle has gone too far to end now!"

With that, Zwei fired another Ice Beam from her hands that struck Zygarde in the chest. At the same time, Mugen fired another Ice Beam that struck Zygarde on the right knee. Zygarde once again shattered the ice that had formed on its body and started to glow with a brilliant green light. Suddenly beams of green light shot up from the ground where Mugen was standing and the earth shattered apart beneath him. The lights faded and Mugen was out cold.

"Now Galatea! Fleur Cannon!" Amber and Zwei commanded.

The end of Galatea's right arm transformed into a cannon, and she fired an intense beam of pink energy from her tree up at Zygarde. The attack struck Zygarde in the right side of its chest and caused it to stagger back five steps. Zygard recovered though and once again glowed with a brilliant emerald light. Green lights then began to shoot up from the ground under Galatea's tree, and suddenly the ground shattered and the tree toppled over. Galatea was knocked out of the tree and hit the ground, totally unconscious.

Amber telekinetically deployed the pokeballs for her two fallen Pokemon and called them back in. Soon after the balls returned to Amber's hands, Zygarde fired another blast of energy from her chest. This time Zwei took the attack head on. A large Z of green light formed from the resulting explosion. Amber felt the full force of the attack due to her link to Zwei and was nearly knocked out of the sky. When the smoke cleared from the explosion though, both Amber and Zwei were still in the air.

"We're not… going to fall to you!" Zwei and Amber declared together.

Suddenly Amber's keystone began to glow with a strange gold light. Both Amber and Zwei called out, and suddenly Amber's body began to shin with a brilliant gold light and her hair turned from green to a shimmering gold. At the same time, Zwei's body turned gold as well and small bolts of crackling blue electricity sparked around her. Zwei spreak her arms and a ball of gold energy that was eight times her size formed in front of her.

"Psystrike!" Zwei and Amber called out as the feline launched the ball at Zygarde.

The sphere struck Zygarde and caused a massive explosion of white light. The shockwave from the blast nearly knocked the yellow news chopper that had been filming most of the battle out of the sky. After a few moments, the light from the explosion finally faded. Zwei and Amber had returned to normal and were still floating in the air breathing heavily; both their brows covered in sweat. Meanwhile the smoke cleared to reveal that Zygarde was still standing.

After a moment though, green lights began to drip from Zygarde's body, and in seconds parts of the humanoid dragon's body seemed to be falling apart. It seemed that the cell creatures that made up Zygarde's body could no longer hold together. Amber and Zwei watched as Zygarde slowly faded to nothing and the green lights falling from it vanished into the ground. Within a few more moments, Zygarde was totally gone.


Not far away, Lysandre's ship had since moved closer to the park where the battle had been taking place. Both Lysandre and Alain had seen the finishing blow that Zwei had inflicted. Malva and Mairin had also since returned and had seen the final attack.

"No… NO!" Lysandre shouted. "This isn't what was supposed to happen! Nothing should've been able to defeat Zygarde or break my control over it!"

"It's over, Lysandre," Alain told him.

"…No it isn't. My vision of a beautiful world will still come to pass," Lysandre declared as he pressed a button on his gauntlet.

Suddenly the bottom of Lysandre's ship opened up like a flower. Inside was a large black cannon with a long barrel that had glowing lines of multicolored light running up the sides. The cannon rotated upward and took aim at Amber and Zwei.

"Even without Zygarde, I still have the power to remake this world!" Lysandre declared. "And I'm going to start by wiping out that wretched clone girl and her Mewtwo off the face of it!"

Lysandre pressed another button on his gauntlet, and a ball of multicolored light began to form at the end of the cannon's barrel. Both Amber and Zwei noticed the cannon charging up. Amber snapped her fingers, and suddenly Alain, Mairin and Malva vanished from the ship with a flash of blue light, reappearing seconds later down in the park. The blast forming at the end of the cannon continued to get larger, and suddenly Zwei launched another Psystike attack at the ship. The attack struck the cannon, and suddenly the entire ship exploded into a massive fireball.

"My god!" a horrified Alain spoke.

Zwei finally returned to her original form, and both she and Amber landed on the ground a few feet from where Alain and the others were.

"How could you?" Alain shouted at them.

"Lysandre was going to destroy us," Amber told him. "We had no choice but to eliminate him."

"Couldn't you have found a better way?" Alain asked. "What Lysandre did was evil, but… but still…"

"You admired him a great deal, didn't you Alain?" Amber realized. "His actions must've been a great betrayal to you. I can understand how you feel, you know. I felt deeply betrayed when I found out that Dr. Fuji thought of me only as an experiment, that I wasn't his real daughter but a clone."

Alain clenched his fists at his sides. "I want to know one thing now, Amber. Do you still intend to try and conquer the world?"

"Of course we do," Zwei answered. "Nothing has changed our ultimate goal."

"Then I'll stop you!" Alain declared. "This may have started out only as a mission given to me by Lysandre, but I've now truly seen just how dangerous you both are! I'm not going to let you roam free!"

"You're welcome to keep coming after us, Alain," Amber told him. "I look forward to our next encounter."

With that, Amber and Zwei vanished with a flash of blue light. Soon after the duo teleported away, Mairin glanced back and saw a man standing a few feet away. He was extremely tall with very long unkempt white hair, wearing an orange ski cap with a long green scarf, a tattered black jacket, a grey sweater, and blue jeans with black boots. He had a pair of fingerless black gloves on his hands. A large black pack was on his back, and a strange gold key hung from his neck by a chain.

Mairin went over to the man out of concern and curiosity. The man had a look of what seemed like total amazement on his face. He was looking at the spot where Zwei and Amber had vanished.

"Mr., are you okay?" Mairin asked. "Were you here for that whole battle?"

The homeless man didn't look at Mairin and kept staring at the spot where Amber and Zwei had been. "That Pokemon and its trainer… I've never seen anything like them before. Such power… only the strength of the Delta could hope to defeat them."

"Huh?" Mairin responded.

"Not my concern though," the homeless man continued as he turned around and started to walk off. "They destroyed my old weapon. That's what matters now. Maybe now you'll finally come back to me… won't you Floette?"

Mairin continued to watch as the homeless man walked away and vanished into the trees. She couldn't figure out what to make of him.

"Mairin, everything okay?" a voice asked. She turned to look to see Alain standing behind her.

"Uh, yeah. I guess so," Mairin answered. "I was just talking to this weird guy I just saw. I'm a little worried that he might've gotten caught in Amber's battle with Zygarde and hit his head or something. He was talking about some strange stuff. Then again, it didn't look like he was hurt, so…"

"Well… right now we should probably leave," Alain told her. "We need to figure out a plan to capture Amber before she causes any more harm."

"You got it," Mairin replied, and with that they left the park with Malva.


Amber and Zwei teleported to a small forest a good distance from Lumios City. Both of them were totally exhausted. Amber sat down against a tree and took off her sunglasses to wipe the sweat from her brow.

"That battle really was more difficult than I thought it'd be," Zwei declared. "You were wise to have Galatea and Mugen assist us."

"Zygarde was the most challenging opponent we've faced yet, and we're stronger for defeating it," Amber responded.

"So what now?" Zwei asked.

"Now we get to a Pokemon Center to rest," Amber answered as she got back up. "Mugen and Galatea both need to be tended to, and you as well. Once we're all back at full strength, we'll return to Saffron City and continue to look for Mewtwo Ein there. I'm certain he'll show up there eventually."


When Alain and the others returned to Lysandre Labs, they found Professor Sycamore waiting for them out front. The professor went into the lab with the trio, where Alain and the others filled them in on everything regarding Amber and Zwei, and on how Lysandre had gained control of Zygarde.

"I just don't believe it," Professor Sycamore spoke after hearing everything. "To think that Lysandre found and hired the scientist that created Mewtwo to repeat his work, and that he had created a human psychic clone as well."

"Lysandre didn't know anything about Dr. Fuji making another clone of his daughter to serve as the second Mewtwo's partner until after she went rogue and destroyed Dr. Fuji's island," Malva informed the professor. "We should still have Dr. Fuji's project logs on record, if you'd like to see them."

"And all of this so Lysandre could test out this synthetic Mega Stone he had created," Professor Sycamore spoke. "Lysandre was a genius, but also a mad man. The events of today have proven that."

"Professor, you should know that I had no idea at all about what Lysandre was planning with Zygarde," Alain told him.

"I know that Alain, and it doesn't really matter," Professor Sycamore replied. "What matters now is tracking down this Amber Drei. From everything you've just told me about her, she and that Mewtwo of hers are just as dangerous as Lysandre was, if not more so."

"They seemed to get stronger during the battle with Zygarde," Alain added. "Just before Zwei launched her final attack on Zygarde, she seemed to turn gold."

"Not only that, Amber's hair turned gold as well," Malva interjected.

"Do you have any idea what caused Amber and Zwei to transform like that?" Mairin asked the professor.

"It's hard to say," Professor Sycamore answered as he put his hand to his chin. "I'm only guessing right now, but it could be that the two of them tapped into a new level of Mega Evolution."

"A new level? Do you really think such a thing is possible?" a surprised Alain asked.

"Well, there's still a bit about Mega Evolution that we don't know yet," Professor Sycamore pointed out. "This is all just theoretical of course, but it could be that the strong bond between Amber and Zwei allowed them to tap into a hidden power."

"Do you think there might be others who could tap into this level of power?" Alain asked.

Professor Sycamore looked Alain in the eye. "It might be possible. Like I said Alain, this is all just theory right now, but it wouldn't surprise me if others could reach this same level of Mega Evolution. It all depends on the bond between the Pokemon and its trainer."

"This is all well and good, but this doesn't get us any closer to figuring out how to catch Amber and Zwei before they try to conquer the world," Malva pointed out.

"Do you have any ideas about that Ms. Malva?" Mairin asked.

"Well… there is one," Malva answered. "Maybe the answer is to fight fire with fire. Come with me."

Malva led Alain and the others into the corridors of the main lab building and took them to a metal door at the end of a hallway with a keypad. The pinkette entered a code into the keypad, causing the door to slide open. Inside the room on a steel pedestal was a metal belt like the one worn by Zwei with a blue stone fitted into the large buckle.

"Another Mega Stone?" Professor Sycamore observed.

"Lysandre made two synthetic Mega Stones, both of which he was sure were compatible with Mewtwo," Malva explained. "He decided to call them Mewtwonite X and Mewtwonite Y. Lysandre gave the Y version to Dr. Fuji for his early experiments. Had Amber and Zwei not gone rogue, Lysandre probably would've given the X version of the stone to Dr. Fuji to try out."

"But how is this Mega Stone going to help us stop Amber?" Mairin asked.

"Simple. We give it to the original Mewtwo to use," Malva answered as she turned around to face them.

"Hold on! First of all, we don't even know where to find the original Mewtwo," Alain pointed out. "Let alone whether or not it would actually help us. Second, it would need a trainer to help trigger the power of the stone."

"I may have an idea about where to at least find Mewtwo," Professor Sycamore told them. "A lot of the Mewtwo sightings seem to take place in Saffron City in the Kanto Region or the nearby cities."

"Why would Mewtwo go there?" Mairin asked.

"Wait a sec… the leader of the Saffron City Gym is a psychic, right?" Malva asked.

"Yes, Sabrina. Her psychic abilities are reported to be extremely powerful," Professor Sycamore answered.

A smirk appeared on Malva's face. "Then maybe that's why Mewtwo likes to hang around Saffron City. It must find a human with extreme psychic powers like its own to be very interesting."

"You think Sabrina and the original Mewtwo actually know each other?" Alain asked.

"It's a long shot, but right now it's the only lead we've got," Malva answered. "And if we're right about Sabrina and Mewtwo being friends, than we also have a potential trainer to trigger the Mewtwonite X."

"So then what do you propose we do?" Professor Sycamore asked.

"To start with, I'm going to take this Mewtwonite X and make a trip to Saffron City," Malva answered. "Sabrina and I are going to have a little talk."

THE END


Author's Note: I hope everyone reading enjoyed this episode. There was certainly a lot going on in it. I had debated with myself about Zwei and Amber's golden transformation during the battle and whether or not to use it. By the way, I'm sure that those of you who've played the X and Y games recognized the homeless guy that Mairin talked to after the battle.

Well, one more story to go before I wrap this up. Next time, Amber and Zwei find out that it's not always a good idea to meet your heroes.

Until then, please review and let me know what you think.