I always figured the Matrix (complete with Zion and the machine war backstory) was just a VR game for humanity to keep ourselves occupied with while we waited for <world event X> to happen in the real world. (Colony ship to arrive, global warming to reverse itself, radiation to die down, whatever.)

Or even (plot twist!) for all the people in the Matrix to be sims / ems in a game, with the agents being actual humans playing the game, who of course have superpowers and a mysterious overarching goal because what video game character doesn't?