Also there's a hint from the rainbow rocket episode, as the team leaders there were all from alternate universes where they had succeeded in their goal, and Giovanni has a Mewtwo.
I'm not keen on this whole "piece together the story for yourself" where you have to really go out of your way and explore to find out what happened thing that Gen 1 had going on either tbh. But it's ironic that when Zelda do it for BotW, most people (not me) loved it.
I always assumed they wanted to catch Mewtwo after it escaped from Cinnabar Island.
Mt Moon they were after the fossil Pokemon to sell off to try and raise funds for the operation, or just for more strong Pokemon.
Lavender Town they are looking for Ghost Pokemon as the only Pokemon at the time...
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