Okay, my memory is bad and I tend to really mess things up when I summarize things, but for those that need to know, here's MY version of Matrix: Revolutions.
It starts off with Neo still in a coma in the real world. However, in what turns out to be a place between the real world and the matrix (called the train station), Neo wakes up. He is greeted by a young Indian girl and her parents. Her parents are programs, but they fell in love and created the little girl. Because she was created under these unusual circumstances she is a program without a purpose, and so is slated for deletion. Her parents don't want that so they are trying to smuggle her into the matrix, where as you remember all the rogue programs go to escape deletion. BTW, the Merovingian (funky french dude) controls the train station. Neo is stuck here in this Limbo. This whole sequence seems interesting but doesn't really go anywhere.
Back in the real world, all the ship captains are trying to figure out how the machines defeated them so throughly, and they suspect Bain (who Agent Smith now somehow inhabits). They get a call from the Oracle. When they visit her, they see that she has changed forms (you probably already know that the original actress who played the Oracle died). She explains that she changed form because of some choices she made. This is just my thought here; in the previous matrices the Oracle fulfilled her role as another level of control; just someone to point the One towards the source to reboot the matrix. However, this final time she decided to help the One in a different way, because she knew the old way of doing things just led to more uprisings and this choice somehow changed her form. Anyhoo, the Oracle tells Trinity, Morpheus, and Seraphim (the guy who guards the Oracle) to see the Merovingian about freeing Neo from the Train Station. They go to the club that the Merovingian owns, and after a cool fight scene, demand the return of Neo and end up picking him up from the train station.
Both Neo and Bain wake up from their comas, and Neo says he needs to rest for a while. When he comes back, he says that he needs to take a ship to go to machine city. All the ships are supposed to head the opposite way, so of course one of the captains objects. They ask him if the oracle told him to do this, and he says no, he just knows he needs to. Only Morpheus trusts his judgement on this, but it's Naiobi who lends Neo her ship. Trinity decides to go with him.
So here the story splits in two; you got the attack on Zion and Neo's quest. The Zion battle is pretty spectacular. Basically the Zionists fight off wave after wave of squiddies, but soon are overwhelmed by the shear number of them. Just as the machines are about to penetrate Zion's defenses, the ship carrying Morpheus, Naiobi, and the others (the group that split from Neo) comes in and launches an emp bomb, which disables all the attacking squiddies, but at the same time it disables all of Zion's defenses. A new swarm of squiddies starts an attack, and Zion is all but helpless. Just as they are about to destroy Zion, they all stop. They are awaiting orders from the main machine, who is talking to Neo.
Backtrack a bit to Neo and Trinity. They are flying to machine city, but little did they know that Bane stowed away on board. Trinity leaves the bridge of the ship to check on something, and Bane knocks her out. Bane goes up to the bridge to kill Neo. He greets him as "Mr. Anderson" and talks exactly like Agent Smith. Neo is bewildered. "Who are you?" Who else calls you Mr Anderson, ya big dummy! For a maddening 5 minutes they banter back and forth, and Neo just can't figure out who this guy is. I guess it is confusing, as the movie never explains how Smith is able to exist in the real world. They fight, and Bane ends up blinding Neo with some electrical wires. At this point Neo uses his "second sight," and he sees Agent Smith as a flaming wraith. Neo ends up beating the hell out of Bane. Trinity comes up to the bridge after all is said and done. Gross visual of Neo's melted eyeballs.
Brief side note: Smith is taking over the Matrix by copying over all the inhabitants. He even takes over the Oracle. He wants to destroy everything, because that is now his purpose.
They finally arrive at machine city. The machines chase Neo and Trin, but after some fancy flying they crash past the defenses and land in the city. During the crash Trinity is impaled on some pipes. In a somewhat ridiculous 10 minute death scene, Trin tells Neo that there was no saving her this time. She lived long enough to give him the strength to get to this point, but she had to die or else Neo wouldn't be able to do what he had to do because of his attachment to her. They kiss, she dies, he goes to see the main machine (I think it's the architect as he appears in the real world). A bunch of small machines gather to form a big talking face, much like the sand face in The Mummy. Neo strikes a deal with the machines; let him destroy Smith in exchange for peace. The machines agree, knowing that Smith is too dangerous and out of their control.
Neo is back into the Matrix, where Smith is everywhere. However, only the alpha Smith (which is the one that took over the Oracle, BTW) will fight Neo. They have a huge fight, but in the end, no one can get the upper hand. Smith gets frustrated, and asks why Neo keeps trying, keeps getting back up, keeps fighting when he knows he's going to lose. Neo says "Because I choose to." They fight some more, and then Smith starts saying some weird things, and then saying "why did I say that?" It's the oracle, who is still active inside of the alpha Smith. She gets out a final message through Smith; "Every beginning has an end." It finally dawns on Neo that he'll never defeat Smith by fighting him; Smith in his current form exists as the antithesis of Neo; one is the savior and the other destroyer. As long as Neo lives, so will Smith. Neo knows that he must sacrifice himself. He just stands there as Smith takes over his body. Then, all of the extra Smith's starting blowing up, much like Smith did at the end of the first Matrix. After the Smiths explode the bodies revert to whoever they were before. The alpha Smith blows up, and Neo's body collapses, apparently dead. The machines leave Zion alone, and the war is over.
Back to the Matrix. It has been rebooted. The Oracle is walking along, and the little girl from the beginning comes out. She says she wrote a sunshine program for Neo. I guess she has some kind of power that she can manipulate the matrix in some way. She asks the Oracle if they will ever see Neo again, and she says they almost definately will. Some people think that the little girl is the next "One." The architect (Colonel Sanders) comes out and talks to the Oracle. The new deal is that the humans that wake up from the Matrix will be allowed to leave freely. Those that are already outside no longer have to fight, and those that are stuck inside will remain so (free choice, the central theme of all the movies). The Oracle asks how she can trust that the architect will keep up his side of the bargain; he sneers and says "What do you think I am, human?"
In the end, I enjoyed the movie, but wished they addressed all the cool stuff they alluded to in the second film. In fact, the second film has almost no consquences in the third film. The fact that there were previous matrices doesn't really matter; the Merovingian in little more than an annoyance in this film. The one thing that does carry over is that things happened just the way the architect said they would. Neo returns to the source, carrying the new debugging code with him, inserts the code and reboots the Matrix. I'm guess that when he took the cookie and candy from the Oracle in the first and second films, she was inserting into him the new code to fix the Matrix. This code is what destroyed Smith in the end. Although Neo, Trinity, and Morpheus were important players, it basically boils down to a battle between the Oracle and Architect. The Architect has only one function; to balance the equation of the Matrix, to create order. The Oracle seeks to unbalance the equation with the randomness generated by human free will. She is the Architect's antithesis.
Well, that's this Matrix Nerd's view o' things.