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I don't think he came from the GBA/DS timeline, since he had an Audinite in his pocket, but I do believe he was on some kind of mission on SS Anne, and in the end the ship sank (in RBYFRLG there is an NPC who claims to be from the International Police. so who knows?)
Also, the game happens around 10 years before XY, maybe he recovered those memories in some point... All we know is that 3 years later he was in Sinnoh with his Croagunk (probably caught it in this region), and some point later, but before XY, the poor pokémon died
