Quote Quoting Stay Puft (view post)
I'll throw this in to the conversation, based on having played the Matrix Online for a short while (which the Wachowskis did say was canon at the time, although if I was to wager a bet Lana probably forgets The Matrix Online ever existed haha):

Immediately after the events of Revolutions, the Matrix is rebooted (as seen in the final scene of Revolutions) and the Machines uphold the peace treaty (as The Architect promises): those who want to stay in the rebooted matrix do, and those that want to leave are disconnected and sent to Zion. The Matrix Online is interesting in this context because the story is actually about resurrecting Neo and his RSI, so in a way the Wachowskis already kinda did some ground work (but again, I'll assume Lana ignores this and takes the ideas in a different direction). Morpheus leads an opposition movement in the newly rebooted matrix and creates new tensions between Zion and Machine City because the machines renege on one of their promises: they refuse to return Neo's body to Zion (iirc, they recycle Trinity's body). Morpheus demands the return of Neo and various factions start to come into conflict over this: some humans continue to distrust the machines and attempt to salvage Neo's RSI to resurrect him in the matrix, while rogue programs (including The Merovingian, as well a faction of rogue Agents) start waging their own wars. Eventually, Morpheus is assassinated by one of these rogue factions (presumably, The Merovingian) and the peace treaty between Zion and Machine City begins to crumble. That's where I stopped playing but from what I understand the peace eventually ends and war resumes, and the humans try to reassemble Morpheus's RSI to bring him back as well, while The Merovingian apparently becomes the "big bad" of the whole thing, figuring out how the matrix itself works and waging war both within and without (as I recall, you played as a "red pill" in the game with your own custom RSI and could actually choose to align yourself with one of three factions: Zion, Machine City, or The Merovingian). The game wasn't terribly popular in the end and it got shut down long before these story arcs resolved.

Anyways, it was a neat game partly because it played a lot with the concept of RSIs (residual self images) which the movies never really got into much (particularly with WB shooting down ideas like Switch using their RSI to swap genders). Based on the trailer for Resurrections, I'd wager that RSIs will actually be prominent in the new movie as well (we see that with Neo in the mirror, etc.) and again I'm doubting Matrix Online is canon but it still points to ideas that Lana will probably still use, namely: Machine City kept Neo's body and plugged him back into the matrix (he's being fed blue pills by NPH to manipulate his RSI, for example) while Trinity may or may not be alive (based on Matrix Online, she would have to be a resurrected RSI iirc but Machine City could still have her body) and Morpheus almost certainly is "dead" (the recast could suggest he's a reassembled RSI like in Matrix Online or simply another program). That's as far as I'll speculate, though I find it curious (again) that The Merovingian is also back in the new movie and I'd wager his role will remain consistent with what we've seen even in the game (he's still the leader of a massive crime syndicate, still a rogue program that wants to kill the Oracle, and I'd bet like in the game he now exerts influence outside of the matrix itself).

It's fun to reflect on this now; I have to admit, the nostalgia hit me in waves while watching the trailer. I don't get hyped for blockbusters anymore but I was obsessed with The Matrix back in the day.
From what the trailer looks like, and what you just described, they may just be adapting the game as a film.