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oh damn, I think I figured what happened. If the rocket walks up to fight you then you're able to take the path in the right and talk to mewtwo directly which you weren't supposed to. I'm surprised this hadn't been reported yet but it's a bit too late to fix anything now.
The Giga drain TM is in Johto, somehwere in the goldenrod rocket hideout or the underground, I don't remember exactly.

well i checked and you shouldn't have been able to talk to it directly... lol how did you manage to do it?

I have no clue; sorry I can't be of more help :(

I used VBA if it mattered at all although I'm guessing it didn't

hm, i replayed that section (I hadn't played since crashing it) and it seems like the mewtwo just doesn't fly away when the scientist below it says "oh no, where did mewtwo go". I guess it's supposed to fly away, lol

and yeah, from that point, I can talk to it again and crash reliably.