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I'm guessing it was just this dialogue:

I'd like to think its an alternate world where Giovanni beat the HgSs protagonist/the protagonist wasn't there to stop him during the time travel event but then got caught by Necrozma.

Is there an explanation for Giovanni and Mewtwo?

I assumed the memory loss was staved off because you were with an Ultra Beast... I was also thinking: Since all the other bad guys were from worlds where the protagonist doesn't exist, maybe the Ultra Wormhole areas are just the Alola region where the main protagonist didn't exist and the UB's...

So why do the villains in this game retain their memories but fallers don't?