For the sake of not getting confused, it's probably a good idea if you follow this link to the deleted scene of Pokémon The First Movie. I put in a few things that might be easier to understand if you watched it first so you don't think I'm crazy for slapping in random things.

Pokemon - Origin of Mewtwo.

Username - Ashhterr

(sorry if it doesn't work)

In the deleted scene, when a clone "dies" it disappears completely, body and mind. For the sake of convenience…I ignored that for this story.