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I know you already said you don't know what the problem is, but I just thought I'd mention I'm experiencing the same thing. Defeated the Indigo League. Walked through Pallet happy and what not. etc. Now only the Lab has people in it. Only thing I can't say for sure is if it happened directly...
So, I just got done fighting Mewtwo in Cerulean and caught him with a Masterball. It said I caught him, and the data was entered into my pokedex with the symbol saying it was caught, but he didn't show up in my party even though I only had 5 party members and he's not in the PC. Did I screw...