The Analyst is his own content warning
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A routine health check after a mission uncovers a firewall blocking the same memory from Neo and Trinity. The only problem is that they can’t remember what’s inside. With some expert hacking on their side, the Mnemosyne crew venture into their memories to crack the code…and learn more about their beloved heroes than they ever imagined.
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It's been 60 years since Neo and Trinity's incursion into the Machine City. Neo and Trinity are dead, and while their sacrifice did initially bring peace, a schism soon developed among the Machines, leading to civil war. In the midst of the war, The Analyst rose to power among the Machines and built a new Matrix from which no one has escaped in decades. The human/Synthient alliance is starting to lose hope. Many think that rescuing anyone from The Analyst's Matrix is impossible, but Bugs and their crew believe that they've found a way to break people out, and will go to any lengths to free the rest of humanity from The Matrix forever.
This fic is what I wish Matrix Resurrections had been. Yes, I'm rewriting the whole-ass movie.