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Alright so after the slug fest of a route you finally get to the hideout of the evil guys base. after a few events in the game you can stop their plans and snag a couple of nice Tm's.
They have been empowered by the two dark legend pokes and have been following their commands almost like puppets.
You trash the place in the regular fashion and defeat the lesser admins (Like chris-chan and some other terrible counterpart). And defeat Boss of evil team, his design will come around eventually but he has the poison legendary similar to the Ghetsis fight in B/W.