Mewtwo returns to confront the man who made it a weapon, and this time the question isn't whether it can win, it's whether winning means anything if you're still just doing what someone else designed you to do. Giovanni doesn't want to destroy Mewtwo anymore. He wants to own it again, which means Mewtwo has to choose between freedom and the only purpose it was ever given. The clones force the real question: if you're made for a reason you never asked for, does refusing that reason actually set you free, or just leave you empty.

Giovanni, the leader of Team Rocket, tracks Mewtwo to a remote corner of the Johto region and sets out to capture it again. Ash and his friends, busy trying to save Pikachu from Jessie and James, are seized by Domino, a newcomer to Team Rocket. The clone Pokémon are taken as well and serve as bait to lure Mewtwo in. What follows becomes a contest of will between Mewtwo and Giovanni, while Mewtwo searches for whether it and the clones have any purpose in life despite being made by science. The special mixes action and adventure with drama and some comedy.