The movie starts out with Mewtwo seeing images of Mew. Mew flying around in the mountains and in a lake. The Mewtwo wakes to see 4 scientists studying the tank. Mewtwo realizes he's in the tank and says he needs to be outside. He breaks through the glass and the scientists start talking and congratulating themselves. The head scientist explains that Mewtwo is an experiement of a cloning process of the "aniceint" Pokémon, Mew. Mewtwo questions himself about his destiny. He then denies his destiny as a simple experiement and begins to destroy the laboratory. Giovanni's helicoptor lands on the island. Giovanni wants Mewtwo as a "partner", and explains that Mewtwo will not just control the world without Giovanni's help, he will destroy it. Giovanni offers to help Mewtwo focus his power, Giovanni puts metallic armor on Mewtwo. Mewtwo thinks that this will surpress it, Giovanni denies and tells him that it will "focus" his power. Mewtwo battles a number of trainers, including Gary. He defeats all of them easily, but Mewtwo still wants to know his purpose. Giovanni tells him that his purpose was to obey humans, Mewtwo also denies this, and proceeds to destroy the Gym. Mewtwo flys off the the very island he was created and asks himself who he is, and what his purpose is. He then states that "The Reign of Mewtwo has Begun" thus bringing the title on the screen.
Then, the narrator comes on stating how Ash has strength and a will of steel. Ash sits at the table, "Hungry, ... need food." Misty tells him to get to work, Ash just says he's too weak to work. Brock cooks his "lazy-boy" soup, and tells them it's perfect for Ash. Then a trainer comes up the path and asks Ash if he'd like to battle. Ash immediatly jumps up and gets ready for the match. After a little small talk with Misty, (Misty- I though you said you were too weak to work! Ash- I am too weak to work, but a Pokémon battle isn't work.) Ash starts to battle. The trainer starts off with a Donphan and Ash starts off with Bulbasaur. Ash wins with Bulbasaur using Solar Beam, and the trainer goes onto a Machamp, Ash chooses his Squirtle. Ash wind again with a Bubble Beam. The trainer is furious and attacks with 3 pokémon (Golem, Venomoth and Pinsir) and Pikachu just uses his Thunder attack and fries all three of them. The trainer is in shock... Ash celebrates his easy victory as Team Rocket look on. Jessie, James and especially Meowth are starving, Jessie offers to cook, but Meowth reminds her how terrible a cook she is.
The next scene goes up in the sky as a Fearow flies with a camera around it's neck. Then in Mewtwo's Palace, the missing Nurse Joy asks Mewtwo if he'd like to send an invitation. Without saying anything, (talepathically) she sends for a Dragonite with the invitation. The Dragonite arrives with the invitation, Ash opens it up to find a hologram of a woman. Brock comments on how pretty and familiar she looks. Ash of course says "yes" on the invitation. The Dragonite flys away, only to run into Team Rocket. The Dragonite drops the invitation. Then we see Mewtwo moving his hand(?) and making a storm with his Psychic powers, all as a test for the "chosen trainers". Then a vision of Mew waking below the water in a bubble, then flying into the sky. Finally back to Mewtwo for more storming. Next scene goes to the docks and we see Ash, Misty and Brock running to get away from the storm. At the building, we see a whole bunch or Pokémon trainers with thier Pokémon. When Ash and the gang get there, Officer Jenny tells everyone that the ferry to New Island has been cancelled. Then the harbor manager aggrees saying it could be the worst storm, ever. One of the trainers says he'll just use his Water Pokémon to swim there. Officer Jenny responds by saying if his Pokémon got hurt, then he'd be out of luck because of the disappearance of the Nurse Joy. Brock looks at the picture commenting on how pretty she is, also saying she looks familiar.
Next we see some of the trainers fly off and swim toward New Island. Officer Jenny threatens to put them under arrest, then the harbor manager says that these trainers are fearless and take this as just a new challenge. Also saying this is what put them apart from other trainers, making them Pokémon Masters. Officer Jenny looks at her like she's crazy, then looking on to the trainers.
Ash wants to go to the island with his Pokémon. But Misty reminds Ash that thier Pokémon are too small to take the heavy waves. Then a disguised Team Rocket comes up to the shore in a boat. They offer to give Ash and his friends a ride to New Island. They get in the boat and they notice that they are dressed as Vikings. Ash makes a stupid comment on how the are mostly located in Minnesota. Then a huge wave hits the ship, washing away Team Rocket's disguise. They all get tossed out of the boat, then Ash and Misty get out their water Pokémon and swim up to the water's surface. They see New Island and swim into the cave where the missing Nurse Joy greets them. She asks them for their invitation and Brock finally realizes that she is the missing Nurse Joy from the Pokémon Center. She says that they must be mistaken, that being said, she leads them to the Palace. Then we see Team Rocket pop up out of the water with Weezing. Next is a really cute and funny part with Mew playing with the windmill.
Next we see the Nurse Joy leading them into the Palace, she gets them through the double doors and into the "waiting room". She says that all the people capable of her "master's" presence are her. Ash is shocked that their are only 3 other people. She explains that anyone who braved the storm are worthy, anyone who doesn't, aren't. Brock realizes that the storm was just a test. The woman ignores him, saying for everyone to release their Pokémon. We then see Team Rocket followed them, only to be trapped. Then they see a waterfall in which they can climb in. Jessie notices something, (Mew) but just misses seeing it. James and Meowth ask her what she was looking at, but she then says nothing. Then in the "waiting room" Ash meets the 3 other trainers. One who flew on his Pigeotto, one rode on his Gyarados and one who rode on her Dewgong. Then everything goes dark, Nurse Joy tells them they are about to meet the greatest Pokémon Master in the world. We see Mewtwo hover down to all the trainers. Nurse Joy tells them that the greatest Pokémon trainer is also the most powerful Pokémon. Then one of the trainers comments on how a Pokémon can't be a Pokémon trainer. Then simultaneously, the woman and Mewtwo both say, "Quiet, human. From now on, I make the rules." Then Mewtwo uses his psychic powers and throws the trainer across the room into the water. Then the trainer sends his Gyarados with a Hyper Beam, but Mewtwo just deflects it back at the Pokémon. Then Mewtwo puts the Nurse Joy out of his power. The Nurse Joy falls, but Brock is there to catch her. Mewtwo finally explains tp everyone that he had the Nurse Joy in his power after he transported her from the Pokémon Center.
Team Rocket walk into a room, Jessie sits on a button that activates the "Pokémon Replication System". A robotic hand picks up Meowth and brings him into the machine. James gets Meowth, but not before the computer can pluck three hairs from Meowth. Thus, making another Meowth (a clone) and we see Mew look on in curiousity. Then the computer brings up the recording of the scientists that worked on Mewtwo. Next, we see Mewtwo giving a little "speech" about how Pokémon will never live equally with humans, and says that the trained Pokémon are slaves. Pikachu disagrees by saying Ash is his friend. But that just gets Pikachu thrown across the room, but not before Ash catches Pikachu and takes the fall. Then Ash challenges Mewtwo to a battle, and Mewtwo accepts. He summons his three Pokémon (Blastoise, Charizard and Venusaur) then opens a door revieling a stadium. Brock realizes that this whole thing was planned.
The one boy trainer takes out his Venusaur(Fruit Root), the girl takes out her Blastoise(Shell shocker) and finally Ash takes out his Charizard, saying he has no nickname for it, but as soon as Charizard comes out, it attacks Mewtwo. Mewtwo comments on how poorly trained it is. The two Venusaurs start, "Fruit Root" starts out with a Razor Leaf, the other uses Vine Whip to not only deflect the leaves, but also throw "Fruit Root" across the stadium. Then "Shell shocker" goes up, it uses Hydro Pump, but the other just uses Tackle(?) to deflect the water and knock "Shell shocker" across the stadium as well. Ash uses his Charizard and tells it to use it's Speed, not Power. It flies up in the air, the other flies even faster, and it over-powers Ash's Charizard. Then Mewtwo's Charizard grabs Ash's Charizard and holds it, flying toward the ground, Mewtwo's Charizard lets go and Ash's Charizard smacks right into the ground.
As his prize, Mewtwo takes all the Pokémon to make clones. Ash defies Mewtwo and gets thrown right into Brock. The black Pokéballs go flying after all the Pokémon, Mewtwo looks on with a smile on his face. Ash and the others try frantically to get their Pokémon away, Ash even gets Squirtle and Bulbasaur back into their own Pokéballs, but it's no use. They too get sucked up into the black Pokéballs, however, the biggest chase is with Pikachu. Pikachu goes running up the stairs and Ash follows. Pikachu gets rid of a great number of the black Pokéballs by using a thundershock. But he uses too much energy, and falls off. Ash tries to catch him, but before Ash is able to, one of the pokéballs gets Pikachu. Ash follows it into the little tunnel they go into to be cloned. Team Rocket name the Pokémon that come through, and see Ash. Ash goes in after Pikachu and breaks the machine, but saves Pikachu, but also after Pikachu was cloned. All the clones hatch, and the machine blows up sending all the black Pokéballs on the ground and the Pokémon out safe. The clones arive as Mewtwo looks on to the other trainers. Mewtwo talks of his plan to rule the world with the cloned Pokémon. Then Ash comes out of the smoke saying, "You can't do that Mewtwo, I wont let you". Ash comes out with all the Pokémon behind him. Then, Ash makes a stupid move of running at Mewtwo and trying to throw a punch. But it's deflected my Mewtwo's forcefield, then Ash gets up and tries again, but this time Mewtwo uses his Psychic powers and sends Ash
flying up toward the wall. Before Ash collides, a red bubble softens his landing. Then Mew emerges, the bubble pops and Ash falls on his rear. Mew laughs, and creates another bubble, only for it to be popped by Mewtwo. Then Mewtwo send more enery balls at Mew, then Mewtwo explains that he was created from Mew's DNA.
Ash looks on as Mew and Mewtwo begin to fight. The fight goes on and Mewtwo fires a black energy ball at Mew, it contacts. Then it explodes but a blue energy ball comes back at Mewtwo, and it sends him into the stadium seats. Mewtwo challenges Mew to a battle with all the Pokémon. He explains that he and his powerful cloned Pokémon will triumph with it's superiority. But Mew disagrees saying that true power comes from the heart. Mewtwo blocks all the Pokémon's special abilities with his Psychic power. All the Pokémon begin to battle, except for Pikachu. Ash looks onto all the Pokémon fighting while "Brother, My Brother" plays in the background. It shows the Pokémon kicking, punching, head-butting, bitting, you name it, but Ash's Pikachu refuses to fight. Then, as the trainers look on, they say how useless it is to fight, thus beginning the message of peace. All the Pokémon begin to tire out, and Ash's Pikachu still refuses to fight. All the while Mew and Mewtwo fight in the sky. Ash finally gets down from the wall he was on, and all the trainers still talk about peace and how it's wrong to fight. Mew and Mewtwo go down to the center of the arena, and keep fighting. As of now, the other Pokémon have gotten too tired and stopped fighting. Mew and Mewtwo use their powers and attacks, but right before the final attack, Ash runs out in between the two. When the attack is finished, Mewtwo comments on how foolish Ash was to interfere in the attack. When all clears, Ash has been turned to stone!
Pikachu runs over to Ash, and starts to shock him, all the Pokémon wake up by now. Pikachu keeps shocking Ash until he's out of energy, then Pikachu, along with the other Pokémon, starts to cry. Everyone's tears bring back Ash, and all the Pokémon and Pokémon trainers rejoice as Ash comes to. Mewtwo is just shocked, that "the human sacrificed his life to stop our battle". Mewtwo finally realizes that it was wrong to pit the Pokémon against each other and how it doesn't matter how you were born, but what you do with the gift of life. With that, Mewtwo takes all of the clones and flies away with the message, "I will never forget what conspired here today. What this has left, is best forgoten". He flies away, and a huge blue aura surrounds the Pokémon and Pokémon trainers, and they were sent back in time to where they were still at the harbor. The storm is still there and Officer Jenny still warns them about the storm, but this time, Nurse Joy is here to offer shelter to the Pokémon trainers and their Pokémon at the Pokémon Center. Ash and friends don't even remember how they got there, and suddenly, the storm is perfectly cleared up. They go outside, and see nothing, not even New Island. But Ash does see one thing, Mew, he then comments on when he left for his Pokémon journey, he saw a rare Pokémon (Ho-Oh). Misty says, maybe he's just seeing things. Then we see Team Rocket and how they don't remember anything either. They arrived on an island(an empty one) and they say it's paridise, and how this is finally a happy ending.
Mewtwo Strikes Back
Mewtwo Strikes Back
The Origin Of Mewtwo
Pikachu's Summer Vacation