The special starts out by explaining about Mewtwo from the first movie. (In case anyone missed it) However, Giovanni still wants it for its imense power. He begins by searching out for any clues via satelite photo. He spots Mewtwo on a isolated island in the middle of a lake. Mewtwo stands on a cliff of the island, questioning himself.
The gang walks through the forest and finds a fairly large mesa. Brock explains about it and everyone seems to be surpised. Misty spots a bus going through a trail. However it starts to rain so they try to get to it ASAP. Meanwhile, the notorious Jesse, James and Meowth happen to spy on them. Meowth also explains about the area. The rain grows into a violent storm and blows them away. However the bus came to a stop, the driver talking to a woman in a rain coat. The bus takes off and Brock slides trips while they were coming down, leaving them in front of the woman. As usual, Brock is attracted to her and tries to flirt with her, Misty pulling him out of the picture. Ash still wants to go towards the mesa, which susposed to be a nice spot. The woman however invites them into her cabin nearby to take shelter from the rain.
Meanwhile, the bus gets caught under an extremely high wind and flies off the trail! But something seems to be watching them and stops the bus from flying and sets it onto the ground. Everyone is amazed but the driver. We see who stops it, Mewtwo, and two of his clones, Pikachu and Meowth. Both of them seem to wonder why Mewtwo saved the bus. It seems Jesse James and Meowth have caught themselves on a cliff branch.
Back in the cabin, the woman introduces herself as Luna. She says that the water coming out of the mesa has some strange properties to it and they go out to the balcony that is above a river. Luna lowers a bucket and fills it up with the water from the mesa and puts it in a cup. She hands it over to Brock and he takes a sip, which immidiately loves the taste. Misty tries some and too loves the taste of the water. Ash tries some, but doesn't understand why it's so good, Brock and Misty scolding at Ash. Then Pikachu and Togepi tries some and they both like it. Misty decides they should follow the river up stream in hopes to get to the mesa. While they travel, a cluster of Ledian are in a tree, Misty watching them until she notices the bugs she doesn't like. Kakuna after Kakuna, a Pinsir and some Beedrills, she impusively rows back scared. When they return, Brock notices a large group of Butterfree flying, they watch as well as Mewtwo on his island. The two clones again question Mewtwo and he explains everything to them.
After watching the Butterfree, a knock is heard at the door. Luna opens it to find a man with a teenage girl. Luna recognizes him as Benishrina, girl introduces herself as Domino. Brock again, is attracted to her, Misty pulling him away. Luna asks whats going on and Benishirina explains that water found in the mesa is extremely pure and vitalizes. When both of them were in the middle of talking, Jesse, James and Meowth happens to make their big entrance, Domino wondering why they're here. The three obviously make attempts to grab the Pikachu and succeeds, floating away in their balloon.
They decide to find their way up the mesa. Mewtwo sensing something won't be right. A wind catches Team Rocket's balloon and sends them flying to were Ash and co. are and end up hanging from the balloon. Team Rocket doesn't seem to know how to handle the situations so they continue to go to the mesa. Domino uses her binoculars to look at the island, getting a look on Mewtwo. However the image is sent to Giovanni! Could she be working for Team Rocket?
Mewtwo notices Ash on the balloon and remembers him quite well. Giovanni, now confirmed with its exsistence, heads to the mesa, with a whole army of Rockets.
Domino gives the scoop on who's seen and Giovanni says to head back to him. She climbs the rope, hitting mostly everyone along the way. She radios Team Rocket for back-up and James wonders where's the back-up. Meowth points it out, spotting dozens of lights. Of these lights consists of balloons and a helicopter all going for the island. Everyone climbs back onto the balloon basket, Ash obviously wanting Pikachu back. Benishirina questions Domino why she called up the Team Rocket. She makes a flashy entrances, calling herself 009. (uh...) She has a black rose in her hand all showing off, throwing it at the balloon causing it to pop then makes a fast getaway in a hang-glider. Ash and his friends are thrown off into the lake, Jesse James and Meowth to the island, with Pikachu. Domino returning to the helicopter.
Jesse, James, and Meowth get caught up in the balloon, but James is happy because they have Pikachu. Or did they? Pikachu is on the ground, angry, and then shocking them, until another bolt hits Pikachu's. It was the Pikachu clone from before. Jesse wanting Meowth to translate what the clone is talking about. The clone goes on for a while, then giving Pikachu a few threats. Mewtwo comes by and the clone goes after Pikachu, Mewtwo stopping it however. Mewtwo talks for awhile about clones and the appearence of Team Rocket. Meowth finds himself with his clone. More talking goes on between the clones, everyone worried. (there's too much talking... so that's what basically goes on for a while) Jesse and James become inspired and decides to say soemthing different to finish off their motto.
Giovanni later stating his in chopper that he will get Mewtwo.
Later, Ash and co. walk back to the surface, Ash disappointed about Pikachu. Ash wants to get to the island, but how? Luna suggests a fallen log nearby to made into a raft. Ash sends out Bulbasuar and Chikorita to use razor leaf and make one. Soon they set off, everyone noticing that Team Rockets coming closer.
Later on the island, the Pikachu scolds at the three from Team Rocket, trying a negotiation. This leaves Jesse and James behind bars, Meowth being free. Everyone hurries along back to the surface. A the water-type clones and a few more set out towards the lake to scout.
Meanwhile, Ash and co. make it to the island, heading up some stairs in a dark cavern. They find themselves in a pond area. Benishirina tests the water, which seems to keep things healthy if drank. And the whole island is full of it! A pack of baby Ryhorn and Nidoqueens make their way to the pond for a drink, everyone watching them. It seems like the Pokémon enjoy it here too and prefer solitude.
The scout was comeplete and Meowth seems to be shocked. Just then, Giovanni's helicopter appears from the brush. A cannon-looking thing appears at the bottom of it, firing at a few clones, causing them to be stunned. Which makes them easy to capture. Team Rocket makes their move and starts stealing the Pokémon. Pikachu saves its clone and so does Meowth. They start to run, but is caught in a dead end. Just when it seems to be the end, Mewtwo saves them. He releases the other clones and Giovanni appears in front of Mewtwo.
They exchange names and begin talks about joing Team Rocket. Two machines appear beside Mewtwo and causes a shock, sending Mewtwo down. Mewtwo isn't even flinched. The machines charge up but Mewtwo quickly disposes them. Giovanni still somewhat impressed, but decides to blackmail Mewtwo. Either he joins or the island where the water is will be captured by Team Rocket. Ash and co. try to escape but is caught by Team Rocket and confronts Domino. Jesse and James complaining in their cell, they want in some action as well...
Domino picks up one of the baby Nidoqueen and admires it. Luna telling her that's dangerous, and the mother Nidoqueen leaps at Domino along with Ryhorn. Domino simply throws her rose and it shocks the two severely, and catches them. She tells how ruthlessly she steals Pokémon. Domino finds Jesse and James and gloats how well she works, Jesse being jealous. Again the negotiations are on with Mewtwo and Giovanni. Everyone decides to help Mewtwo if possible. Mewtwo allows them to levitate and they go for the army. Giovanni tells Domino to evac, but is too late, as well as Mewtwo. Once again Giovanni appears and asks again for Mewtwo to join or every Pokémon will suffer more. The two machines from before appear and create a energy sphere. Giovanni gives him a choice, submit, or everyoen gets it. Mewtwo can do a thing about. Domino shows they're not kidding by blasting both Pikachus with her rose. (what's in it?) Mewtwo goes forward, the clones telling him not to, still he does. Mewtwo enters the sphere, but Giovanni doesn't play fair. He shocks Mewtwo so it can't do a thing and...they'll take the island anyways with Mewtwo in their possesion!
All the clones, Ash and co. are sent to the cell. Both Pikachus collaspes and Benishirina gives them the pure water from the pond, both reivie instantly. Domino comes in a bosses them around.
It seems like Team Rocket just wanted a base here. Construction starts everywhere, Giovanni not really satisfied still. What's worse yet, they're making the water bad. This causes a uproar. A large cluster of Ledian and Beedrill head for the island. Every Pokémon sensing this. The Ledian spray their sleep powder on the workers, causing a blow torch to fall in a gas tank. The explosing blows the door free where Ash is and they escape.
The army of Pokémon appear in front of Domino. She simply throws her rose, but some Scyther cuts them. She poles vaults over them, but slips on the floor where Jesse and James were mopping. There she goes... Luna and Benishirina get another water sample, just in case.
Meanwhile Ash, Misty and Brock make it to Mewtwo, who still under the entrapment. Ash and Brock try to throw one machine off, but the focusor just changes. So Mewtwo decides to give it everything it gots to throw of the machines. Both Pikachu use Thunderbolt on one and it blows up. The other blows up as well. Mewtwo is weak, so they decide to get him to the pure water. However, Giovanni blocks their path, but Misty and Brock send out their Pokémon to distract them. Meowth spots Jesse and James and they make a run for it. Ash starts to go and Giovanni tries to pursue, but can't because the water-type clones and the bug-types surround them.
Ash makes it to the pond and finds Luna and Benishirina. Ash has no other choice and throws Mewtwo into the pond. Mewtwo gets a few flashbacks of Mew and talks to himself. Giovanni appears in his chopper, asking for Mewtwo. Mewtwo appears right in front of him, this time it's for real. Mewtwo creates a large beam that destroys practically everything. The lake is gone, Giovanni mad, and Luna and Benshirina wonder where everyone is.
Mewtwo and Ash are in the source of the water. Meowth rushing out from spying to tell his opinion about the clones, then everyone else shares theirs. (some more talking goes on) Mewtwo again decides to erase everyone's memory, only those still oustide. Team Rocket, Giovanni, Domino, Luna, and Benishirina forget everything and wonder why are they were they are. Mewtwo sends the clones off for their own paths. Jesse, James and Meowth in their normal balloon, Ash and co. in a Pikachu balloon. Everyone says their farewells and set off. Mewtwo flying past them, splitting up him, the Meowth, and Pikachu.
The bus again stops in front of Luna's home. The bus driver wondering what Benishirina is doing.
Ash and co. walk through a town, Ash thinking he heard Mewtwo. Mewtwo stands still upon a high flagpole on top of a building