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Two machines, invented by Giovanni, made their appearances in Mewtwo Returns. The Team Rocket boss notes that it required a significant investment to create them.
One is red, while the other is gray. They are meant to turn Mewtwo into Giovanni's puppet, each using an energy orb as a weapon. The first time Mewtwo is encountered by them, it is able to knock them away with its Psychic powers. However, they are not destroyed; instead the machines create an energy orb that Mewtwo is forced to walk into.
Once inside, Giovanni threatens to destroy all the cloned Pokémon. However, even though Mewtwo's can no longer control its own body, its mind is not truly controlled by Giovanni. Seeing this, Giovanni then realizes that Mewtwo's body will be destroyed but decides to keep Mewtwo within the orb to determine whose will is stronger.
Ash and his friends arrive and attempt to deactivate the machines. Even with the help of Pikachu, Meowth and the clones, they are unable to be destroyed. Mewtwo, using the last of its strength, finally destroys both machines.