The gang was on their way to the Indigo Plateau where the Indigo League was going to take place. Ember had trained with her Pokémon on the way there. Right now the gang was setting up the table for lunch. But Ember kept on staring at the sky.

"What's wrong Ember?" Misty asked, "You keep spacing out."

"Sorry Misty," Ember apologized, "The truth is I don't know what's wrong. I have this strange feeling that something's going to happen. But I don't know if it's good or not."

Misty was about to ask Ember a question, when she was suddenly interrupted.

A trainer, which was dressed, liked a pirate, walked up to them. "My name is Raymond and I'm looking for the one named Ember Ketchum," he said "You know her?"

Ember stepped forward. "She's me." she said.

Raymond took out a Pokéball from inside his vest. "Let's do a match," he said "and don't think I'll make this an easy one."

"Okay," Ember stepped forward, "I accept."

Ember's first Pokémon was Venusaur, the final form on her Kanto Grass Starter. Raymond's Pokémon was Donphan; a ground type Pokémon that looked like an elephant which was from the Johto region.

Ember had Venusaur attack Donphan with Razor Leaf, but before Venusaur had the chance, Donphan attacked Venusaur with the move rollout. The move rollout made Donphan roll around like a ball. Donphan kept on rolling into Venusaur and Venusaur didn't have a chance to defend itself. But then Ember had Venusaur use Solarbeam. Being a ground type, Donphan easily got defeated by the Solarbeam. Raymond's next Pokémon was Machamp. Ember sent out Blastoise to battle Machamp. Machamp kept on attacking Blastoise with kicks, but it got beaten by Blastoise's Bubblebeam. Out of frustration, Raymond sent out three Pokémon; Pinsir, Venomoth and Golem. Ember sent out Tesla and Tesla easily defeated Pinsir and Venomoth with Thunderbolt and Golem with Iron Tail.

So Ember won and Raymond lost.

Ember started cheering over her victory with her Pokémon and Misty and Brock began congratulating her. Then a Dragonite arrived to where Ember and the gang were, it gave them the invitation. The invitation was a hologram of Mewtwo's servant talking about her master wanting to have a Pokémon battle with them and asking them to come to New Island. There was also a card that Ember had to answer yes or no to. After saying yes to the invitation, Dragonite flew back to New Island.

That afternoon Ember and the gang arrived at the port, where the ferry for New Island was. At that moment a huge rain storm appeared. The sea was getting rough too. At the pier, there were a lot of Pokémon trainers, waiting for the ferry to New Island. But there was a problem. The harbor master and Officer Jenny declared the ferry to New Island cancelled. Ember knew that the storm was Mewtwo's doing; he was using his psychic powers to bring forth the storm.

"The harbor master has declared that this is the worst storm ever." Officer Jenny explained.

The harbor master started telling everyone about a legend that took place a long time ago; a fierce storm attacked a town and killed everyone except a few Pokémon. Those Pokémon were filled with sorrow and cried out tears. Then magically those tears brought everyone to life.

A male trainer named Fergus refused to back down, "Well I'm going to New Island anyway. All my Pokémon are Water-type! We'll just swim over to that palace!" He said.

"l warn you, the waves will be savage! You will never make it!" The Harbor Master warned.

"lf you try that stunt and your Pokémon got hurt you'd be out of luck because we closed the Pokémon Center." Officer Jenny warned.

"How come?" Ember asked.

"The nurse in charge of the center disappeared last month. lf any of you see her, please contact me at once." Officer Jenny pointed to a picture of the missing Nurse Joy on the wall, "That's a picture of her over there on the wall."

Brock had a look of the missing Nurse Joy on the poster and blushed, "She's cute." Then he took another look at her, "She sure looks familiar."

Even though the storm outside was terrible, it did not stop Ember and the gang and three other trainers from getting to New Island. One male trainer, named Corey, used his Pidgeot, Fergus used his Gyarados, and a female trainer, named Neesha, used her Dewgong.

"Some trainers have no fear. To them, this is just one more challenge. They follow their hearts. That is what sets them apart and will make them Pokémon masters." The Harbor Master said.

Ember brought out her shiny Gyarados. "Rory, we need you to give us a lift to New Island." she said. Then she turned to Officer Jenny and the Harbor Master, "Don't worry, we'll be fine."

The harbor master nodded, "Good luck to all of you."

Ember nodded back. Misty put Togepi in her rucksack for safety. She and the gang climbed onto Rory. Rory managed to get Ember and the gang through the ocean safely. They did stay underwater, so the waves wouldn't hurt them, but they go up sometimes for air. And then at last they finally reached New Island.

The sea around New Island wasn't rough; in fact it was like New Island was the center of the storm. When the gang got onto the dock of New Island, they saw the woman from the holographic invitation.

"My master bids you welcome to New lsland," she said, "Please present your invitation."

Ember showed her the invitation and the hologram of the woman appeared, "The bearers of this invitation may be admitted to New Island."

"Hang on a minute," Brock interrupted, "Aren't you the Nurse Joy missing from the Pokémon center?"

"You do look just like her." Misty said.

"I'm afraid you are mistaken," The woman denied, "I have always been my master's servant. Please, come this way. My master awaits your arrival."

Ember knew that the woman really was Nurse Joy, but she was being controlled by Mewtwo. Ember knew that she and the others had to be careful from this point.

The woman led Ember and the gang to a big dining hall, where Corey, Fergus and Neesha were.

"I guess the other trainers couldn't get here through the storm." Ember guessed.

"Yes," The woman said, "You and those other trainers were brave enough, in my master's eyes, to get here through the storm."

"Are you saying that the storm was some kind of test?" Brock asked, shocked.

"That is correct. Now please release your Pokémon from their Pokéballs and join the others." The woman requested, "It won't be long before my master's intentions are clear."

"Guys, don't send out all of your Pokémon." Ember whispered to the others.

"Why?" Misty whispered.

"Something doesn't feel right here. Just keep one Pokémon out." Ember advised.

Ember only had Tesla and Levina out. Brock had Vulpix. Misty had Togepi and Psyduck. Then they walked over to the dining table, where Corey, Fergus and Neesha were sitting.

"I see you guys got here just fine." Corey said. Corey's Pokémon were Pidgeot, Hitmonlee, Scyther, Rhyhorn, Sandslash and Venasaur.

Fergus's Pokémon were Gyarados, Seadra, Vaporeon, Golduck, Tentacruel and Nidoqueen.

Neesha's Pokémon were Wigglytuff, Ninetails, Dewgong, Rapidash, Vileplume and Blastoise.

When the introductions were done, the lights suddenly went out.

"You are about to meet my master." The woman announced.

Just then a dark figure floated down towards them.

"Raichu Rai. (I don't like this feeling.)" Tesla and Levina ran over to Ember and climbed onto her shoulder. Togepi went over to Misty and she picked up the little Pokémon.

"Yes, the world's greatest Pokémon master is also the most powerful Pokémon on Earth. This is the ruler of New lsland and soon the whole world, Mewtwo." The woman announced.

The lights came back on and revealed Mewtwo. Ember stared at Mewtwo with wide eyes.

'Mewtwo.' She thought.

She never knew that Mewtwo would be so intimidating up close. But it wasn't his appearance that intimidated her, it was his aura which screamed 'anger'.

"A Pokémon can't be a Pokémon master!" Fergus shouted, "No way!"

"(Quiet, human.)" Mewtwo ordered through telepathy, "(From now on, I'm the one who makes the rules.)"

"It's Psychic!" Brock gasped.

Just then Mewtwo raised his hand, glowed blue and lifted Fergus into the air. Fergus screamed in pain and everyone else gasped at this. Mewtwo flung Fergus into the water fountain. Fergus was cross with that and sent his Gyarados to fight Mewtwo.

"We'll show you! Let's go, Gyarados! Use Hyper Beam!" Gyarados fired the hyper beam from its mouth, but Mewtwo used the move counter, which made hyper beam bounce right back to Gyarados, giving it a lot of pain.

"Ah, Gyarados!" Fergus swam over to Gyarados to see if it was okay.

"(Child's play.)" Mewtwo turned to his servant, "(Your usefulness has ended.)" he said.

The woman started to faint and Brock caught her. Then the woman's hat fell off her head, revealing herself as the missing Nurse Joy.

"Where am I?" She questioned, "And how did I get here?"

"(You have been under my control. l transported you here from the Pokémon center to serve me.)" Mewtwo answered, "(Your knowledge of Pokémon physiology proved useful to my plan. l have cleansed your tiny human brain of memories from the past weeks.)"

"Who are you?!" Brock shouted at Mewtwo.

"(I am the one who will be the ruler of this world and the master of humans and Pokémon alike.)" Mewtwo announced to everyone.

"You're not the ruler of this world, Mewtwo. That job already belongs to the Pokémon." Ember declared.

Tesla nodded, "Rai!"

"(You humans brought me into your world to make me become your slave)," Mewtwo said to them, "(But now I will take my revenge by destroying your world and make a world only for Pokémon.)"

"So you hate humans and you plan to destroy us to save Pokémon." Brock stated.

"(No)," Mewtwo shook his head, "(Your Pokémon will not be spared. They have disgraced themselves by serving humans. Your Pokémon are nothing but slaves.)"

Tesla jumped off of Ember's shoulder and stood in front of Mewtwo, "Raichu! (You're wrong!)" She said.

"(So you say that I'm wrong?)" Mewtwo asked.

Tesla nodded, "Rai rai raichu. (I'm not Ember's servant and never will be. I'm her friend and family.)" She told him.

"(You're not this human's servant, you're her friend? You're pathetic! Humans and Pokémon can never be friends.)" Mewtwo used psychic to lift Tesla and threw her.

Ember caught Tesla before she could hit the ground.

"Ember!" Brock and Misty called out.

"I'm fine," She told them and looked up at Mewtwo, "Don't pick on my family."

Corey sent his Rhyhorn to attack Mewtwo. Rhyhorn was about to use Tackle on Mewtwo, but Mewtwo blocked Rhyhorn with counter and sent it flying.

"(Fools, my power is too great. No trainer could defeat me.)" Mewtwo told them.

"Then how about a real match? A Pokémon battle?" Ember stepped forward.

"(Is that a challenge?)" Mewtwo asked.

"Yes it is." Ember replied.

Mewtwo's eyes glowed, then a Venasaur, Blastoise and Charizard came through the floor.

"(I began with Squirtle, Charmander and Bulbasaur like any other trainer)," Mewtwo explained "(But with their DNA I was able to create powerful copies of their final evolved forms.)"

"That means they're clones." Corey said.

Just then Mewtwo revealed a Pokémon stadium to everyone. Corey introduced his Venasaur, nicknamed Bruteroot. Neesha introduced her Blastoise, nicknamed Shellshocker. Ember then released Natsu her shiny Charizard.

Corey battled Mewtwo first. He had Bruteroot use Razor Leaf to attack Venasaurtwo. But Venasaurtwo used Vine Whip to slash the leaves away and then picked up Bruteroot and toss it to the ground.

Neesha went up next. She had Shellshocker use Hydro Pump against Blastoisetwo. But Blastoise easily avoided the attack with Rapid Spin and then used Rapid Spin again to knock out Shellshocker.

Ember went next, "Okay Natsu, let's go!"

"ROAR!" Natsu roared at Charizardtwo.

Then the two took the skies and both of them attacked each other, non-stop for about five minutes.

Ember pulled out her Key Stone necklace from under her shirt, "Not too bad, but can you handle a Mega Charizard?" (She always wore around her neck, but it was hidden underneath her shirt next to the Rainbow Feather)

"(Mega Charizard?)" Mewtwo asked.

"That's right." Ember placed two fingers on the Key Stone as it glowed.

The Mega Stone on Natsu's necklace glowed.

"Key Stone, let our hearts become one," Ember said, "Go beyond evolution. Mega Evolve!"

Ember's shiny Charizard Mega Evolved into Mega Charizard X.

Everyone was shocked at Charizard's new appearance.

"Mega Evolution." Corey, Fergus, and Neesha said in awe.

"(What is this?)" Mewtwo asked.

"It's called Mega Evolution. It can only be achieved when a trainer and Pokémon have a Key Stone and Mega Stone. They're bonded as one and that bond enables them to go beyond their evolution and into Mega." Ember explained.

"(That's impossible! Humans and Pokémon can't bond like that!)" Mewtwo protested.

"We'll see about that." Ember stated, "Natsu, Blast Burn!" She called out.

Natsu roared and then punched the ground, causing cracks to stretch all the way to Charizardtwo and an explosion behind it erupted from below, causing a massive explosion.

When the smoke cleared, Ember's shiny Charizard was still standing and in his original form. Then they noticed that Charizardtwo had fainted.

"(Impossible! How can your Charizard be stronger than my clone Charizard?!)" Mewtwo demanded.

"Natsu and I along with my other Pokémon have been through a lot together. None of them would never back down from a fight." Ember stated as her shiny Charizard smiled before she returned him to his Pokéball.

"(Fine. However I'm still the victor)," Mewtwo said, "(I shall claim my prize; your Pokémon.)" He created some black Pokéballs and used them to catch Bruteroot and Shellshocker.

"Bruteroot!" Corey exclaimed.

"Shellshocker!" Neesha cried out.

Misty and Brock quickly returned their Pokémon to their Pokéballs.

"What are you going to do with the Pokémon?!" Misty demanded.

"(l will extract their DNA to make clones for myself. They will remain safe on this island while my storm destroys the planet.)" Mewtwo said, calmly.

"You can't do this!" Brock shouted angrily.

Mewtwo created more black Pokéballs and used them to catch everyone's Pokémon, except Togepi. Ember followed the Pokéball that captured Tesla and Levina to the lab, where the Pokémon were being cloned. Then all the clones began walking out of the lab. Ember managed to set the real Pokémon free from the black Pokéballs.

"Everyone we have to stop Mewtwo and his clones." she said to the original Pokémon and led them out of the lab.

At that time Mewtwo welcomed his cloned Pokémon.

"(With my clones, I shall obtain the world.)" Mewtwo declared.

Just then Ember, with the real Pokémon, walked in. "I can't allow you to do that, Mewtwo." She said.

All of a sudden Mewtwo used Psychic to lift Ember up and flung her away. Ember was just about to crash into a stone wall, when suddenly a big pink bubble appeared and saved her. Then Mew, the Ancestor of Pokémon, appeared before her.

"Hello Mew." Ember greeted.

"Mew~" Mew tilted her head cutely.

"Thanks for breaking my fall, Mew." Ember thanked Mew.

"Mew~" Mew giggled.

When Mewtwo saw Mew, he tried to attack her with Shadow Balls. But Mew used Teleport to dodge all the Shadow Balls.

"(Mew, we finally meet.)" Mewtwo eyed the Ancestor Pokémon.

"Mew~" Mew looked at Mewtwo.

"Mew?" Fergus questioned.

"It's actually Mew." Brock said, amazed.

Mew giggled at them.

"(l may have been cloned from your DNA but l will prove that Mewtwo is better than the original.)" Mewtwo told Mew, "(Superior to Mew.)"

Mew looked at Mewtwo, "Mew~"

"Mew and Mewtwo." Corey said.

"So Mewtwo was cloned from Mew." Neesha said.

Mewtwo was surrounded by a purple aura, "(This world is too small for two of us.)"

Then he flew after Mew who fled. A Shadow Ball hit Mew, sending it into the clouds. Mewtwo chuckled. Then an attack hit Mewtwo, sending him into the stadium seats, causing an explosion. When the smoke cleared, Mewtwo had a barrier around him.

"(So you do have some fight in you. But l have no time for games. Destiny is at hand. Who will rule? My super Pokémon?)" Mewtwo questioned in a taunted tone.

All the clones called out.

"(Or your pathetic group of spineless inferior Pokémon?)"

"Mew~" Mew was on the side of the original Pokémon.

"(We were created with powers far stronger than the originals.)" Mewtwo stated.

"Mew Mew Mew Ew Ew Mew Mew Mew (You don't prove anything by showing off a lot of special powers and a Pokémon's real strength comes from the heart)." Mew reasoned as she flew around.

"(My clones don't need their powers to prove their worth.)" Mewtwo threw another Shadow Ball at Mew who dodged it. Almost hitting Ember who dove out of the way when she saw Mewtwo summoning up another Shadow Ball. She continued climbing down to get to the others.

"(l will block all the Pokémon's special abilities using my psychic powers. Now we shall see who triumphs. Go!)" Mewtwo commanded.

The cloned and real Pokémon charged at each other; they didn't use attacks like Water Gun or Flamethrower. What they just did was tackling, scratching, punching and biting each other.

Nurse Joy watched the scene with sadness, "Pokémon aren't meant to fight. Not like this." She stated, "lt's useless. What can come out of it?"

"Nothing but pain." Neesha responded.

"Can't Mewtwo understand it's not right to force Pokémon to battle?" Brock commented.

"They're all living creatures. This just proves that fighting is wrong." Misty said.

Ember couldn't help but watch in horror as the Pokémon fought against one another. The fight was terrible; it was like a war, but for Pokémon. The humans didn't like this. Even Team Rocket, who was also watching the fight, didn't like it. The Pokémon were all getting weaker and weaker by the second. Ember was climbing down as fast as she could.

Meanwhile Mew and Mewtwo were charging at each other. Right now they were blasting Psychic at each other. All the Pokémon were really hurt and the Psychic attacks were making everything worse. At that moment, Ember didn't care or remember what happened to her male counterpart in this scene, she just wanted to stop all the Pokémon from fighting! She got down from the stadium seats and ran between Mew and Mewtwo, "STOP!" She yelled out.

Suddenly Ember got hit by Mew and Mewtwo's psychic blasts.

"(Fool, trying to stop our battle.)" Mewtwo said.

"Raichu! Pika! (Ember!)" Tesla and Levina ran over to Ember.

At that moment Ember turned into a stone statue. Tesla tried to wake Ember up with Thunder Shock, but nothing worked. She tried again and again until she realized that Ember was gone, dead.

Misty fell to her knees as tears began to gathered in her eyes, "Please...no." Her body shook as tears fell from her eyes. Brock knelt down next to her and held her close.

Tesla's ears flattened down as she and Levina started to cry, "Rai-Rai...Raichu." Tesla cried sadly.

Misty, Brock, Nurse Joy, Corey, Neesha, and Fergus began to cry. Both the real and cloned Pokémon started to cry for Ember as well. Then suddenly, like magic, the Pokémon's tears began flying towards Ember and went into her body. All the trainers watched as the tears went towards Ember's stone statue.

"These are the Pokémon tears that the harbor master told us about." Brock said.

Mew and Mewtwo watched in amazement of what was happening. After all the tears went into Ember, she began glowing blue and then a light from the sky shone onto her. Almost like a light from heaven.

Tesla and Levina watched silently as Ember's body turned to normal.

Ember opened her eyes slowly and slowly tried to sit up. She looked up and saw Tesla staring at her.

"Tesla, Levina." She smiled.

"Raichu!/Pikachu! (Ember, you're alive!)" Tesla and Levina exclaimed and jumped into her arms.

Then Ember felt her Pokéballs shook and one by one her Pokémon came out themselves: Lucario, Romulus, Venusaur, Natsu, Rory, Blastoise, Boltund, Ignado and Pidgeot.

All her Pokémon cried, roared, screeched, and howled loudly happily. They were glad that their trainer was alive.

Then all of the clone and original Pokémon nodded at each other and joined the happiness cry as well.

Corey, Neesha, Fergus, Nurse Joy, Misty, and Brock all smiled in relief, happy that Ember was okay.

"(The human sacrificed herself to save the Pokémon.)" Mewtwo watched Ember and her Pokémon, "(l pitted them against each other. Only when they set aside their differences did l see the true power they all share deep inside.)"

"Mew~" Mew nodded.

"(l see now that the circumstances of one's birth are irrelevant. lt's what you do with the gift of life that determines who you are.)" Then Mewtwo used his Psychic powers and lifted his cloned Pokémon into the air.

"Mewtwo," Ember called out, "Where are you going?"

"(Where my heart can learn what yours knows so well. What transpired here, l will always remember. But perhaps for you, these events are best forgotten.)" Mewtwo replied.

And then they were gone. Suddenly a light surrounded Ember and everyone and then they all disappeared.

Everyone ended back at the Pokémon Center, but no one had any memories of New Island, Mew and Mewtwo or of the Pokémon battle. Ember knew that Mewtwo didn't want anyone to remember of what had happened. But she still remembered though; so she decided to keep it all a secret; she knew that no one would believe her if she told them.

"We better get our Pokémon check out." Misty suggested.

Brock nodded, "Yeah."

Ember told them that she wanted to go outside for a while. She was at a quiet area as she and Tesla watched the clouds clear from the sky.

Suddenly, the Ancestor of Pokémon appeared in front of her.

"Mew!" Ember quietly gasped.

"Rai!" Tesla gasped.

Mew giggled at them.

"Mew, what are you doing here?" Ember asked.

"Mew Mew Mew (I would like to go with you, Ember)." Mew said.

Ember blinked, "Really? Are you sure?" She questioned.

Mew nodded happily. "Mew Ew Mew Ew Ew Mew Ew (I would like to thank you for helping Mewtwo. I also like you as well. So can I come?)"

Ember smiled and took out a Cherish Ball that Prof. Oak gave to her, "I'll be happy for you to come along with me, Mew. How about I name you Keiko? It means 'happiness child'."

Mew blinked at her new name and nodded, "Mew Mew! Mew Mew Ew! (I love it! I'm now Keiko!)"

Ember tapped Keiko with the Cherish ball and was sucked inside without a fuss.

When Ember headed back to the others, they saw Brock and Misty ready to go. Before they were about to leave, Ember decided to look up at the sky once more.

'I have a feeling that I will meet Mewtwo again.' Ember thought. "I wonder." she said.

"What do you wonder, Ember?" Misty said.

"I'm wondering if I will end up running into any more surprises on my journey." She replied.

"I think you might," Brock stated, "Besides we have run into interesting surprises in the past."

"I agree." Misty agreed.

Ember smiled at that.

Then Ember and her friends decided to continue on their journey.

Pokémon on hand: Raichu (Tesla)(F), Lucario (M), Venusaur (M), Pikachu (Levina)(F), Shiny Charizard (Natsu)(M), Blastoise (M), Pidgeot (F), Shiny Gyarados (Rory)(M), Dusk Lycanroc (Romulus)(M), Boltund (M), Alolan Marowak (Ignado)(M), Mew (Keiko)(F)

Prof. Oak's Lab:

Mienshao (F), Glaceon (F), Leafeon (F), Jolteon (F), Sylveon (F), Shiny Umbreon (Mani)(M), Sandslash (M), Gengar (M), Butterfree (M), Pink Butterfree (Momo)(F), Primeape (M), Cinderace (M), Delphox (F), Kingler (M), Muk (M), Magnenot (Genderless), Nidoking (M), Nidoqueen (F), Shiny Suicune (Azure)(F), Scyther (F), Marowak (F), Dewgong (M), Persian (F), Seadra (F), Ninetales (F), Eevee (F), Kangaskhan (F), Arcanine (M), Rapidash (F), Tauros (9), Porygon (Genderless), Flareon (M), Vaporeon (F), Shiny Rapidash (Comet)(M), Clefable (F), Wigglytuff (F), Aerodactyl (F), Espeon (F), Shiny Farfetch'd (F), Dragonite (F), Aurorus (Aurelius)(M), Aurorus (Istas)(F), Alakazam (M), Midday Lycanroc (Lupa)(F), Midnight Lycanroc (Tynan)(M), Steenee (F), Lurantis (F), Shiny Carbink (F), Trumbeak (M), Alolan Ninetales (Elsa)(F), Alolan Sandslash (Eirwen)(M)