Matrix, the end: you have to believe.

davextreme attempts to clarify the end of the movie and actually it makes sense to me.
Warning: if you haven't seen the movie this might spoil it.

So by the end of Revolutions we have Smith having corrupted the Matrix to a point where the machines can’t stop him. We have Neo, who in choosing the wrong door has broken the cycle necessary to reboot the Matrix, and then we have the two of them destroying each other and leaving the Architect with no idea what to do. Nothing like this has happened before, as shown by Sati bringing color to the sky of the Matrix for the first time ever. By saying that those still in the Matrix will be free, the Architect is pointing to the Christian promise that our bodies will be returned to us at the end of days. What bothers me is not this ending (which I think I like), but that it’s an ending which even the omniscient characters in the story don’t understand. They’re for the first time ever in a situation where the don’t know what’s going to happen, so it just doesn’t feel complete.

And, of course, it isn’t complete. The Matrix is still running in some fashion, and from the press material The Matrix Online will take us into that world. My guess is that it will finally be the battle to convince everyone to wake up, now that the machines don’t have utter control over the world. I’d guess also that The Merovingian and the other rogue programs may have an opportunity to gain a foothold in the anarchy.