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The truce did indeed come to its end - long story. Unfortunately, we never got much in the way of closure. Months before SOE pulled the plug, the game's sole remaining writer - who also did the missions, events, and hand animated the last cinematics - quit. They chose not to hire a replacement, so the story was left in limbo. He did post a summary of what would have happened, however, from his notes. The final fate of things - skipping really convoluted plot threads - would have seen a new arrangement. A new Matrix is created, wherein the human occupants could shape their own reality, cared for by the Machines, rather than enslaved. This would only be for newly grown humans - the old would remain in the previous Matrix. I guess Zion would be again free to free those who chose to take the red pill? Or perhaps there would still be conflict. It's more than a little sketchy. I'll post a text dump of the summary, which goes back to a bit before the Truce was broken, so there's overlap between what was actually ingame and what was planned. I can answer any specific questions you may have.
The last moments of the game's life itself mirrored that of the end of the beta test - all player characters imploded oragami-style (often called the meatwad effect by players), but I think it's safe to say that isn't meant to be canonical.
Wait a minute. He wasn't lying! This isn't even a polygraph. Its a seismograph. We've been having an EARTHQUAKE.