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Leon first appears in Resident Evil: Retribution, so he and Alice have never met before, yet she asks him “So you’re working for Wesker?” Indicating that they’ve met before.

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  • Or indicating she's heard of him, or she's guessing, or other possibilities. – Meat Trademark May 8 at 18:52
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The entire film series is (arguably) about identity, doubt and self discovery. It's also about fighting forces you don't understand alone - versus as a part of a team.

Alice's initial discovery of her situation in the mansion with amnesia, and subsequent ambiguous and frightening discoveries, that lead her to a better understanding of her own past and it's significance within the "big picture".

Memories have been overwritten, characters have been cloned and programmed with basic memories "to ensure correct functioning" as is remarked (by Aida Wong) about the 50 basic models cloned to populate this simulation in the Ex-Soviet submarine pen.

The actual quote from Leon and (this version of) Alice is:

How d'you end up working for Wesker?

To me it seems driven by friendliness, in the first moment Alice feels safe to chat as the team is there, and curiosity about Leon's history, as it might give Alice more clues about the big picture relating to how everything came about, and her own story which is as yet unresolved.

Perhaps it might also tell her if the person claiming to be Leon - her rescuer - is genuine and what he seems to be or just a programmed clone - but that's just pure speculation about Alice's thoughts on my part. (Within the context of a few minutes before Alice and Aida having been attacked by Valentine's security team with many people on it that Alice had known before, but who'd had different loyalties). The film is also, perhaps most strikingly, about trust.

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