Mewtwo first opens his eyes inside a tube to find several scientists staring at him. He ponders his purpose. He hears the scientists talking outside and determines that he should be free of the tube. He has visions of Mew as he's blowing the tube into shards. The scientists tell him a bit about himself (he was a clone of Mew and they want to run tests to see how strong he is) and then begin congratulating themselves and each other. Mewtwo thinks about how he was a clone, a shadow of Mew He doesn't think the scientists are very nice people because of their lack of consideration for his feelings. His anger builds as the scientists continue to talk among themselves. He tells them how angry he is and destroys the lab.
If you can't see the thing following the mouse around, try hiliting the text and putting the cursor on top of the dark part.
Giovanni has been watching from a helicopter, and touches down near Mewtwo. He persuades Mewtwo to come with him by saying that they will be partners and offering to teach him to control his powers. Mewtwo agrees, and the next scene is somewhere in Giovanni's hideout. Mewtwo is being fitted with armor, but he doesn't understand how the armor is helping him. It feels so heavy. Giovanni tells him that it's helping to focus his powers. Mewtwo battles many pokémon, including Gary Oak's Nidoking and Arcanine. He later asks Giovanni about his purpose. In a show of arrogance, Giovanni tells Mewtwo that he was created by humans and will never be their equal. Mewtwo gets angry and blows up the hideout. He returns to the island where he was created.
Near the ocean, Ash waits at a table for Brock to finish cooking lunch. He complains that he's too hungry to work, seeing that he hasn't eaten since breakfast. Pikachu and Togepi are having fun when they see a man approach. The man challenges Ash to a pokémon battle, and Ash jumps up, excited. The man sends out Donfan, a ground type pokémon. Ash sends out Bulbasaur. Donfan starts off well, and sends Bulbasaur flying with his rolling tackle attack. Bulbasaur defeats Donfan by firing a Solar Beam. The man sends out Machamp, and Ash sends out Squirtle. Once again, the challenger's pokémon starts winning early on in the battle. Squirtle responds with Bubblebeam, which faints Machamp. The man is furious, and sends out Pinsir, Venomoth and Golem all at once. Ash sends out Pikachu, who fries them easily.
From above, a woman asks, 'Shall I extend an invitation to these trainers as well?' The answer is apparently yes (you can't hear anything), and she responds, 'As you wish.' A Dragonite flies across the water and knocks over Team Rocket and Ash's picnic. It hands them a holographic invitation, and they say yes.
Mewtwo moves his hand in circles, and the weather gets worse and worse. Soon, there is a huge storm.
At the place where the ferry is supposed to take them to New Island, Officer Jenny and another woman are standing, barring the doors. It is announced that the ferry has been cancelled because of the storm. Three trainers use their pokémon to cross the waves. One uses Gyarados, one uses Dewgong and the other uses Pidgeot. Partway through the journey, the Pidgeot turns into a Fearow, or at least that's how it seems. Anyway, back at the docks, Ash is discouraged. None of the group's pokémon are strong enough to carry them through the waves. Team Rocket comes along dressed as vikings, and offers them a lift in their boat. After some time, the waves become too much for the tiny craft to handle, and the boat tips over in the waves. With quick thinking, Misty calls out Staryu, who swims Misty and Brock to the surface. Ash, on Squirtle, surfaces near them, and they make their way to the island together. Team Rocket shows up a moment later.
As Ash and company walk into the main room of the palace, they are surprised to find only 3 other trainers there. Mewtwo uses the woman to introduce himself, then releases her. Brock catches her just before she hits the ground, and finds her to be Nurse Joy, who has been missing from the pokémon center. The trainers are outraged to find that Mewtwo is a pokémon, and challenge him. He wastes no time in beating all the pokémon the trainers send against him, as well as dissing humans and the pokémon they own, because he thinks them to be stupid to let themselves be enslaved. After a show of power by clones of the 3 evolved forms of the starting pokémon, Mewtwo releases custom pokéballs which steal all of the trainers' pokémon. Pikachu runs from the thief balls, occasionally shooting electricity to keep them away. He is eventually caught, but Ash follows the ball containing Pikachu into a laboratory very like the one Mewtwo destroyed.
Mew shows up at the palace and, after having much fun on a windmill, comes inside. Mewtwo talks about how he will finally get to prove that he is greater, but it's all wasted on Mew who is busy chasing its tail. Mew and Mewtwo begin a small battle, and reach a stalemate.
Meanwhile...
Mewtwo's pokéballs are placed on a conveyor belt leading to a machine which clones them. Ash follows Pikachu's pokéball, and manages to wrest it from the computer's grasp, breaking the machine. All the original pokémon come out of the machine, as well as Mewtwo's clones. Mewtwo calls the clones onto the battle arena by telepathy, and gloats about how the human race will perish while he and his clones will be safe. There is an explosion and billowing of smoke, and Ash emerges from the smoke, announcing that he won't let Mewtwo do that.
A huge battle ensues between Mewtwo and Mew, and the original pokémon and the clones. [All of this happens to the tune of 'Brother My Brother' by Blessid Union of Souls] Pikachu doesn't fight, and although his copy beats him, calling 'Pi ka chu!' Pikachu just stands there. When his copy collapses from exhaustion, Pikachu holds him comfortingly.
Ash sees Pikachu standing and not fighting, and races out to where Mew and Mewtwo are shooting great blasts of energy at each other. He calls 'Stop!' Ash reaches the center of the stadium at the same moment Mewtwo and Mew's attacks converge. Ash slowly turns to stone and falls to the floor. Pikachu runs over as everything stops. Mewtwo mutters, 'Fool... he tried to stop us from fighting,' but it's clear that he is surprised and a bit unsure. Pikachu shakes Ash, and shocks him with electricity, but Ash stays solid as, well, rock. Pikachu heep zapping him until he has no more energy, then starts to cry 'Pikapi...' (Ash...) His tears fall to the ground and are quickly absorbed into the soil. All the other pokémon begin to cry as well, and their tears sparkle as they head towards Ash's body. Pikachu cries one last tear, and Ash returns to normal. They hug.
Mewtwo floats his clones away from everything else, and Mewtwo, Mew and the clones fly off into the distance. Ash calls out, asking Mewtwo where he's going, and he replies, 'I'm going to try to learn what your heart already knows so well. Perhaps the events that took place here are best left forgotten.' A portal opens up underneath everyone, and they are back at the port, with no clue as to how or why they got there.
Ash and his friends go outside to see the last of the storm disappear, and Ash catches a glimpse of Mew floating through the clouds.
The credits roll with scenes of Ash and his friends on their journeys, and they end with a picture of Mew flying towards an island.
Pikachu's Summer Vacation
This short begins with Ash, Misty, Brock and Pikachu standing and looking at a pokémon resort. The trainers all release their pokémon and they go into the resort to the catchy song playing in the background [it's called 'Vacation', and it's done by Vitamin C]. Dexter tells you how he's going into observation mode.
Togepi starts crying because it's hungry. Pikachu begins making faces, which calm Togepi, but is pushed out of the way by Squirtle, who makes Togepi cry. Pikachu desperately tries to calm Togepi, then Squirtle calls him over to an apple tree. An apple hangs from a branch. Maybe it will calm Togepi! Bulbasaur cuts the apple down with 2 well-aimed Razor Leaves. The apple falls onto the ground in front of Togepi. However, Psyduck looks at it blankly, then eats it. Togepi starts to cry again, but is lulled to sleep by Bulbasaur's 'Bulba-bye'.
As Togepi sleeps soundly, A group of 4 pokémon comes along the path, talking and laughing loudly. The group consists of Raichu, Cubone, Marill and Snubble. Squirtle tells them to be quiet, and angers the group. They don't like being ordered around like this. Pikachu tells them to try to set a good example for the baby, and notices Togepi starting towards a log across the river. Pikachu runs after Togepi, and Pikachu's extra weight starts the log rolling. Togepi enjoys the ride, whereas Pikachu is panicked. The log (and Pikachu) falls into the river, but Togepi is safely playing on the other side of the river.
Pikachu walks back to his friends, soaking wet. Pikachu finds them engaged in a one-upping contest. Snubble and Squirtle puff themselves up to see who can be biggest, and Squirtle falls over onto his shell. Then Snubble and Bulbasaur have a face-making contest. Snubble makes himself fall over, his eyes are rolling so fast. Squirtle and Marill have a swimming contest. To start the race, an Electrode uses Explosion. And they're off! [To the song 'Catch Me If You Can' by Angela Via] They're neck and neck at the beginning, but then Marill pulls ahead by going underwater. Unfortunately for Marill, it means going off course, and it runs into a Starmie, who Water Guns it to the other side of the pool. Squirtle finds himself ahead, but is suddenly atop a Goldeen who's going the wrong way! He falls off and swims his hardest, but Marill has won. Ash's pokémon look dejected, while the others are elated.
The 2 groups still aren't finished with each other, though, and Raichu starts shooting sparks. Pikachu runs over to comfort Togepi, and gets hit by Raichu's sparks. Pikachu turns around and shoots off sparks of its own. Raichu and Pikachu push up against each other's cheek, and they start running. They bowl over Team Rocket's pokémon, a Hitmonlee and Hitmonchan, run holes through a hedge maze and run over a napping Charizard's tail. Charizard looks around to see who's disturbed his nap. He spots the electric rodents and races after them. He finally pulls ahead and beats his wings. The racing duo are knocked off the path, right onto a sleeping Snorlax. They don't get up quickly enough, and Snorlax rolls over onto them. They manage to pop out from under it, but fall over from exhaustion.
They start racing again, and Charizard follows. He is so caught up in racing that he doesn't watch where he's flying, knocks over the playground and gets his head stuck in a pipe. He starts roaring and blowing fire, which fries Meowth who is looking down to see the cause of the commotion. Pikachu throws a rope around Charizard's ankle, and all of Ash's, Misty's and Brock's pokémon start pulling with all their might. Charizard is too strong, and with one move of his ankle, knocks all the pokémon over. Raichu and his friends laugh at them. Pikachu comes over and pleads with them to help. After a brief consideration, Raichu, Marill and Snubble decide to help. Cubone, however, decides not to help them. After a little while watching them all pull and struggle, Cubone grabs the rope just ahead of Pikachu and starts pulling too. They finally manage to pull Charizard out of the hole, and he flies up in the air with the rope (and Psyduck) still attatched to his ankle. Charizard lands on Meowth, and Psyduck lands safely beside him. All the pokémon work hard to reconstruct what Charizard broke, then they all have a great time horsing around until it's time to go. All the pokémon go to their trainers, but first Pikachu pauses and offers his hand to Raichu's group. Snubble shakes his hand, and then Pikachu runs into Ash's arms.