Inside the Pokemon Castle located on New Island, a Lizardon, Kamex, and a Fushigibana battle.  The pokemon's Trainers, a group of grunts from the Rocket-Dan, look on helplessly as the pokemon are defeated one after the other.  The pokemon's opponent, a Psychic-Type pokemon named Mewtwo, looks down on his opponents and declares them all too week.  Did they think they could defeat him with this level of power!?  Mewtwo tells the Rocket-Dan to leave him at once and the grunts, scared for their lives, obey.  Some time later, Mewtwo is alone with Joi in a pitch black room, the only light coming from the various television monitors set up along the wall.  "Aren't there any Trainers out there who can make me happy?"


Elsewhere, a Donphan Trainer named Raymond is battling Satoshi's Fushigidane.  Satoshi's pokemon is able to knock out Donphan with a single Solar Beam and so Raymond sends out all his remaining pokemon - Kairos, Golonya, Kairiki, and Morphon.  Satoshi responds by having his Pikachu use one of its electric techniques to attack them all at once.  Raymond runs away, crying for Yama-chan. 

As Satoshi celebrates, Kasumi, who had been looking everywhere for him, angrily approaches him.  "What are you doing!?" she demands.  "The finals are beginning!"  Satoshi, Kasumi, and Takeshi all run to the stadium where the Pokemon League finals are taking place.  Our heroes make it inside just as the winner of the Pokemon League CoroCoro Cup has been decided.  They were too late!


As Kasumi yells at Satoshi for making them miss the battle a dark hole opens up in the sky.  A figure in a cloak riding a Kairyuu comes down from the clouds like a shooting star and immediately demands a battle with the newly crowned Champion!  He then releases three pokemon - a Fushibana, Lizardon, and Kamex, all with unusual stripes on their bodies - to signal the start of battle.  The Champion's Gallop is defeated by Lizardon-Two's Flamethrower, his Parshen by Kamex-Two's Hydro Pump, and his Sandopan by Fushigibana-Two's Solar Beam.  All the Champion is able to do is utter "He's so strong..." as he recalls his pokemon back into their Monster Balls.  The cloaked Mewtwo wonders if this is the level of the person who calls himself "Champion" and decides that the loser has no use for pokemon.  As Mewtwo's ride empties a bag filled with invitations to New Island to the stadium below Mewtwo tells the crowd "Those who want to try fighting me should meet at that island in one week!"  The two of them vanish into the sky.

The crowd begins to talk amongst themselves.  Satoshi, meanwhile, is excited by what just happened and tells Takeshi and Kasumi that he wants to try fighting the self-proclaimed strongest man in the world. 

As Mewtwo and Kairyuu return to Pokemon Castle the Rocket trio are watching through binoculars from a small boat.  They wonder who that is on top of the Kairyuu and decide that it must be the master of the castle.  Kojirou recalls that the island used to be the home to a secret Rocket-Dan laboratory and Musashi adds that that was about half a year ago.  Neither Musashi nor Kojirou can remember exactly what was being researched there but Nyasu remembers hearing that they were studying Mew, the mysterious pokemon of which only one exists in the whole world.  Nyasu also recalls hearing that there was a mysterious explosion at the laboratory six months ago that completely destroyed everything!  Recently it seems like someone's started living there, however, and have even created that huge castle.  The Rocket trio wonders who it could be.


In any case, Nyasu says, they have orders from the Boss to sneak into that castle.  Musashi and Kojirou don't really feel up to it but Nyasu uses its claws to convince them otherwise.

Kairyuu lands at the entrance to Mewtwo's castle.  Mewtwo removes his cloak as Joi welcomes him home.  Mewtwo sits down on a full-body scanner that looks like a reclining chair and tells Joi to give him a full health scan.  As Joi operates the machine Mewtwo looks over at her and asks if his body is different from other pokemon's.  When she says that it is, he then wonders what he is exactly.  A pokemon?  Something else?  Joi responds by flatly telling him that biologically Mewtwo is classified as a pocket monster.  A worn out Mewtwo thinks over what Joi just said as he announces that he's going to rest. 


Deep inside the South American Amazon, a professor named Fuji-Hakase is leading an expedition.  The team, equipped with what looks like riot gear, is closing in on their target.  Fuji-Hakase tells the team to capture Mew no matter what and is even giving the authorization for them to use Master Balls.  The half a dozen or so members of the research team all throw a volley of Master Balls at the newly spotted pokemon but they Mew manages to evade every single one!  A destroyed Fuji-Hakase sees that Mew - his dream - is escaping.  "Wait!" he calls out.  "Mew, wait!"


Mew turns around with a curious look on its face.  Fuji-Hakase and Mew look into each other's eyes.  The other members of the expedition team contact Sakaki on the radio to let him know about the stand-off and ask if they should start throwing their Master Balls at it again.  Sakaki tells them to wait.  He says that since Mew is a Psychic-Type pokemon it could be more intelligent than humans and that it's probably sizing up the professor right now, trying to figure out if it can trust him or not.  Fuji-Hakase, meanwhile, thinks about how he's spent decades hunting for Mew but that he never doubted its existence for a moment.  Mew cocks its head, floats over to the professor, and gives him a hug.  Sakaki, who's watching a live feed of the interaction, smiles.

Later, inside an RV-like laboratory, the professor plucks out one of Mew's eyelashes.  As Mew's DNA's being scanned, Fuji-Hakase lets his mind race with the possibilities the data he's collecting will bring.  He tells the mysterious pokemon that it's the key to the next step in the human race and that with its help humans will achieve more power than ever before.  He then tells Mew that seeing it reminds him of when he was a Trainer himself back when he was young...

Before he gets a chance to elaborate, however, the professor receives a disturbing order: use Mew's DNA to create a brand new pokemon.  Sakaki guesses that Fuji-Hakase's tired of playing Trainer and that creating the world's strongest pokemon is what he really wants to do.  After all, he says, that's the reason he was chased out of the institute, wasn't it?  Because of his "Pokemon Gene Reconstruction Plan"?  The Rocket-Dan will fully support him, Sakaki continues, but then again that's only because Fuji-Hakase's already working for them!  Sakaki laughs.

Later, Fuji-Hakase stares at Mew.  "The World's Strongest Pokemon?"  He thinks back to his colleagues at the institute and all the nasty things they said to him.  "Hahahaha, what are you thinking?" "Pokemon aren't toys!"  "That kind of thinking is trouble!!"  Fuji-Hakase remembers how, after he was kicked out of the institute, the Rocket-Dan came in and set him up with a laboratory of modern equipment and even helped him with his search for Mew.  And how great would it be to show those jerks at the institute the fruits of his labor?  With that, Fuji-Hakase makes his decision.


The professor stares into the test tube housing the new creature's embryo and before long it becomes apparent that he's become obsessed with his new creation.  Mew looks from afar and, with its head hung low, disappointingly floats away.  It takes a while for the professor to realize that Mew has left but when he does he starts to freak out.  Is Mew not coming back!?  But it's OK, he convinces himself.  He'll just make a new pokemon, one that's even better than Mew!  The professor has clearly lost his mind.

Eventually, the world's strongest pokemon "Mewtwo" is completed.  "Mew...two...is that my name?"  The other researchers gathered in the room are shocked that the pokemon can talk.  Fuji-Hakase answers Mewtwo's question and adds that he's someone who can defeat any and all pokemon in battle.  To demonstrate this power the professor has a Nidoking brought into the room.  The Normal-Type pokemon charges at Mewtwo but Fuji-Hakase's creation is able to repel it quite easily.  As Nidoking is flung away a Rocket-Dan grunt is amazed that its power is this great.  Sakaki cackles.

Later, Mewtwo is fitted with a strange armor.  "Fight! Fight! That's what you were born for!" he's told.  "Fight, Mewtwo!"  Mewtwo is made to fight against a number of opponents, all while the professor tells his "son" to listen to his Boss' orders.  Mewtwo says he understands.  Before long Mewtwo is the only one left standing as a pile of unconscious pokemon lie at its feet.


Some time later, Sakaki approaches Mewtwo and tells him that he did well.  Thanks to his actions, he says, the Rocket-Dan's come much closer to its goal of world domination than it ever had before.  Would Mewtwo like anything as a reward?  Mewtwo asks to have his armor removed, saying that it's getting on his nerves.  Sakaki responds by saying that he can't fulfill that request because that armor is a sign of the friendship between Mewtwo and humans.  Mewtwo calls him a liar, saying that he knows that the armor is really just supressing his true power and enabling the Rocket-Dan to use him whenever they want.  Just answer me this one thing, Mewtwo says: Is what I'm doing right?  "Destruction and fighting and plundering?" Sakaki asks.  "Everyone in this world does it. There's no "right or wrong" as far as history is concerned...just winners and losers."

Later, Sakaki is talking to Fuji-Hakase via video phone.  He tells him that Mewtwo is an intelligent being and that he therefore wants him to create an armor that can supresses his thoughts as well.  The professor starts to object but Sakaki says that he wants them to move to Stage 2 of their plan soon: the mass production of Mewtwo!  The time when the world will fall into their hands is coming!

Fuji-Hakase is stunned.  As he stumbles through the dark halls on the way to Mewtwo's chamber he realizes that he's reaching the point of no return.  When he reaches Mewtwo's room the Psychic-Type pokemon seems confused; it's too early for his health check-up, isn't it?  Without saying a word, the professor removes Mewtwo's armor which sets off an alarm elsewhere on the base.


The professor pleads with his creation to destroy the laboratory and everything in it.  Mewtwo refuses, asking how he can be expected to do such a thing to his own father.  Fuji-Hakase responds by telling Mewtwo that, up until that point, everything Mewtwo's known has been framed in the context of suffering.  His parents, his past, other people, the world...he's conditioned Mewtwo to hate all of it.  But if he's allowed to be mass produced, these clones will be mindless weapons devoid of the heart and intelligence that the original Mewtwo possesses.  Tools created solely for war...we can't call such a thing a "pokemon," can we?   That's why, Fuji-Hakase says, he wants Mewtwo to destroy the laboratory and put an end to the Rocket-Dan's ambitions.  It's begging him, as his Trainer...

"But weren't you the one who told me to do what the Rocket-Dan says?" Mewtwo asks. Before the professor can respond members of the Rocket-Dan burst into the room to find out what set off the alarm.  When they see that Mewtwo's free they tell the professor to step away from him.  They then tell Fuji-Hakase that since he's now a traitor he'll have to come with them.  With his back turned toward his creation the professor tells Mewtwo that he had always wanted him to be able to join the rest of the pokemon world someday.  He then thanks Mewtwo for being kind enough to call him "father."


The professor is escorted down the hall as Mewtwo watches.  Two gun-toting grunts stay behind and order Mewtwo to put its armor back on and return to its room.  Mewtwo refuses and, with a mighty burst of his power, destroys the laboratory.  As rain begins to come down Mewtwo falls to his knees and mourns the loss of Fuji-Hakase.  But he has nowhere to go now; he was forced to fight its own kind and so he'll continue to fight.  Mewtwo lets out a scream of anguish.

Back in the present day, Mewtwo continues to rest in its pod.  Tears well up in his eyes as he remembers his troubled past.  A worried Joi looks on.

A week later a storm rages at the port that leads to New Island.  A woman named Voyager addresses the crowd gathered inside to tell them that there won't be any ships leaving for New Island today.  A number of Trainers angrily protest, holding out their invitations and saying they just have to go.  Satoshi, meanwhile, says he won't let some storm stop him.  After all, he says, the world's strongest man is waiting for them on the other side of the sea.  Satoshi runs outside, grabs onto his Zenigame, and hops into the water.  Kasumi says she won't be left behind and hops into the water too.  The other Trainers see Satoshi and Kasumi and decide to follow suit.  Voyager isn't happy.


As the storm rages, Trainers ride their Water-Type pokemon (or, in Takeshi's case, ride in a wooden bucket being pulled by Kasumi's Starmie) toward New Island.  Musashi, Kojirou, and Nyasu ride a metal boat headed toward the island as well. 

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Notes
Mewtwo is explicitly referred to as a male at several points in this adaptation.

Raymond's appearance is based on Raymond Johnson, one of the then-hosts of Oha Suta and the voice actor who portrays the role of a similar character in the movie.  The "Yama-chan" (山ちゃん) that Raymond calls out for as he runs away is a reference to Yamadera Kou'ichi, the co-host of Oha Suta and the voice of Mew.

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