Kind of like a rewritten version of the Matrix: Revolutions, only Zion's actually underneath this large network of giant wooden support beams keeping the surface of Earth up. And Neo and Trinity spend time with their families on Christmas before the machines get to Zion in the Matrix. And something goes wonky with the Machines, involving Agent Smith, leading to several misguided humans to try and launch attacks on the machines on the surface with amphibious ships, that are destroyed by Sentinels the instant the whole thing with Smith is worked out, for a little while anyway. Trinity still dies or at least appears to, only while Neo (who is blind) is hooked into the Matrix on their ship and is yanked back when said ship crashes. Neo still meets the Machine "God" (who looks like a gigantic grey Tonka toy) and still offers to go into the Matrix to defeat Smith for the Machines. The Machines agree because that is what Neo was designed to do, and Neo asks how do they know that?
The Machines created a program within the Matrix to counter the One anomaly and try to balance the system, like balancing an equation. This program was only activated when the One did the unthinkable and chose the door Neo chose. Neo is not "The One", but merely part of an equation called "The One", an equation to balance the Matrix. This program was never intended to be released, but it was when Neo left the Architect. Neo is now both side of the equation, to bring balance to the Matrix when he himself destabilized it (this part made my head hurt).
The Machines provide Neo with enhanced digital armor and a digital cyborg tiger to help him out, and he and Smith and the tiger have this massive free for all battle with the humans in the power pods glowing several different colors before it's over, ending with one of the Smiths and Neo destroying the Oracle-Smith, as this Smith was the boss Smith until the Oracle-Smith was born. Zion survives by faking the Machines out with a transmission from a captured Sentinel that they've already been destroyed, before the result of Neo and Smith's battle (the Machines all short-circuiting) takes place.
And then the dream ends. Weird, huh? Thoughts?