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You're right, and I'm glad they changed that in LGPE. Still, between the Master Ball and the movie, it was a very popular theory that Giovanni was after Mewtwo.

The fact that Team Rocket were after Mr. Fuji always implied some connection to Mewtwo, or at least along with the first movie (that Dr. Fuji died and never became Mr. Fuji, but they didn't randomly pick the same last name for both characters). The extra FRLG references made it obvious, and...

It was just Giovanni, and if we go by LGPE, he hadn't been hiding there for very long when the player showed up: I'll grant you that wearing his usual attire in the gym wasn't smart, but he probably didn't believe anyone could defeat him. He was a cocky bastard. LGPE did throw Trace and Blue...

This was revealed in LGPE and isn't surprising: It's pretty clear that Team Rocket found Fuji's documents regarding Mewtwo and wanted Silph Co. to reproduce his experiment somehow, maybe for all sorts of Pokemon. But the president wanted none of that, and Red saved the day before things got...