Saw Matrix: Revolutions over the weekend. It didn't live up to its potential but I thought if you combine Reloaded and Revolutions, it was one good 3 hour movie. Not great, but good. The Matrix will certainly go down in history as one of the greatest science-fiction movies but the other two will probably just be thought of as not-as-great, which is how sequels used to be thought of anyway. Here's my take on it, put here really for no reason other than to help make my thoughts on it more cohesive. I should say that I have no special knowledge so all of this could be totally wrong. I don't think so though, I didn't think it was too hard to piece a lot of this stuff together. A lot of people seem to be going out of their way to misunderstand things though so that's a problem with a lot of the reviews I've seen.

Smith/Bane - When the humans go into the Matrix, they're basically uploading their brains into code in the system. Smith had the ability not just to copy his code over other program's code, but to merge with it. Smith copied/merged with Bane and when Bane's code was downloaded back into his brain, Smith's code was with it and rewired Bane's physical brain, hence the scarring and weird neural patterns the doctor saw.

Neo outside the Matrix - Neo had power over the machines in the Real World because part of him was still in the Matrix. They said as much when the doctor said Neo's brain waves looked like he was jacked in but his body was obviously on the table. Why he could communicate with his Matrix-self is just one of those All Powerful Hero things that doesn't really need to be explained more than 'he has a connection to the Source'.

The Choice/The End - When Neo met the Architect, he was told to make a choice between A) Destroying Zion, choosing new people to make a new Zion and restarting the Matrix to get rid of the anomaly B) Going back into the Matrix, letting the anomaly run its course and destroy the Matrix, its inhabitants and most of the machines (The Architect: "There are levels of survival we are prepared to accept"). Because he had love for Trinity, the first One to do so, he chose B to save her rather than saving the human race. The anomaly was Smith, the Oracle said he was Neo's opposite, the balance of the equation. Since Neo saved Trinity, she was able to pilot the ship and go with him to the Machine City and meet 1A (the machine leader). 1A knew Neo was the only way to defeat Smith without restarting the Matrix and having the same anomaly pop up again so it jacked Neo into the Matrix and in exchange, stopped the machines from killing Zion. Of course if Neo had failed, the machines probably would have killed everyone. The Oracle set it up so Smith would find her and absorb her, just as Smith said. When Neo was defeated, Smith thought that was the end because he couldn't see past Neo's next choice, to give up. Neo realized, with the help of the bit of the Oracle that came though and told him it was the end, that he had to sacrifice himself to save the Matrix. He let Smith merge with him, which gave 1A a conduit into Smith and all the other Smiths (they all knew everything the Oracle/Smith knew so they had to be connected). 1A destroyed the Smiths and in the process killed Neo. The machines fixed the destruction Smith had caused (the 'deja vu' with the cat on the sidewalk) and with the Smith code removed from the system, everyone woke up as themselves. The Oracle said they would probably see Neo again, continuing with the Messiah references throughout the movie. Presumably the rest of the story is that the humans in the Matrix are told of the true reality and those that want to leave, do. The continuation of the peace and the rebuilding of the world are for the next movies/games/whatever.

There are a lot of unanswered questions:
Was the Merovingian something special or just an old, powerful program? Some think he was a previous One but I wouldn't think so. Why would the Architect let an old anomaly live into a new version of the Matrix when the old one was restarted specifically to try and fix the anomaly? I would guess he's just an old, powerful machine program.

What was Seraph and why did the Merovingian call him 'the prodigal son'? It seems that he was an old machine program, which is why he had gold code when Neo looked at him. I would imagine the Oracle and the Merovingian would have had gold code too if we had seen Neo's POV. His relationship with the Merovingian is probably just one of those things thrown in to make the world more real to the audience. It might be explained in a later game/movie.

Why could Neo "see" Smith inside Bane in Flame Vision? No explination. Just one of those 'connection to the Source' things, even though Smith's code wouldn't have been connected to the Matrix inside of Bane unless he had Neo's same power to be in both places at once.

I can't help but think that a talented co-writer or editor couldn't have tightened up the scripts for both movies and cleared a lot of things up. Pages like this shouldn't really be needed but at the same time I don't think it's bad to leave some thing unexplained. They just left too much unclear here, it makes it harder for a lot of people to enjoy.