/* I have deliberated about where to place this writeup for a couple days. I was originally going to put it in its own node entitled Why people don't like the Matrix sequels, so that should give you an idea of where this is heading before we even leave the gates. In the interest of creating a more complete node and a less fractured nodegel, you can see that the little writeup that could found it's way here. */
Apparently, a large part (enough for me to be writing about) of the movie-going population enjoyed the first Matrix but felt that the Brothers fell down on the job for the sequels. Although not always true with movies that are designed to be trilogies from the start, The Matrix is a well encapsulated story unto istelf. The story entire, across all three films, can almost be seen as a separate story from the first one alone. The reasons are two-fold : the success of the first movie allowed them a complete freedom economically and conceptually in the two sequels, and second the complexity of the plot is greatly increased. Naysayers are often unable to answer to satisfaction the following question :
How does Neo destroy Agent Smith?
The Oracle lets Smith take her, and make her a part of him. He asks a very important question of her : 'If you knew I was coming then why are you here?' Good question! For some reason this program that sees the future just as easily as the present wants Smith to take her. She knows it will help in some way, but how?
Notice that even though there are many Smiths, the original Smith still seems to be the leader of the pack. He is the voice of the beast, or the head. When this Smith takes the Oracle, he gives her (who's now a Smith) a pained look and the new Smith/Oracle laughs maniacally. Could it be that the Smith/Oracle is the new leader?
Neo and Agent Smith are opposite sides of the same coin. The Architect's flawless (and yet ultimately doomed) system is fixed when the Oracle realizes that free-will is an intrinsic part of human nature. Humans can't live without it. So then the Matrix that we know has to have a (randomly and sometimes wildly) varying element that manifests as the One. The system as it is designed can only continue if Neo voluntarily gives himself (his programming/code) back to the Matrix.
However, in this cycle of the Matrix (six I believe, counted from subsequent incarnations of the first One) the One is both Neo and Smith, who has mutated as a result of the combination of both Neo and Smith's genes (programming/code - gee, see a pattern?) into a virus of sorts.
Neo must still merge back with the Matrix in order for the system to continue, yet obviously he was unwilling to sacrifce Trinity in the devil's bargain at the end of Reloaded.
In effect, Neo is still able to merge back with the Matrix (or the Source, if you will) after bargaining a truce with the Machines. Smith has become as dangerous to them as to the Humans. He is a cancer that they can no longer cut out of their "body" without destroying themselves.
Remember that Smith now is the Oracle, Architect, and all the sentient intelligences in the Matrix? He is now in effect the Source.
When Smith "absorbs" Neo, Neo goes back to the source, and the code that can sustain the Matrix system is functional once again. But of course, the Matrix still has Smith-cancer. Luckily, Smith is Neo whether he would admit it to himself or not. When the two merge, it as if two pieces of an original are fit back together and the original piece results, perfect as it was originally designed to be, and the salvation of the Matrix. This saves billions of human lives while his bargain with the deus ex machina saves Zion. It amazed me how the Brothers tied such a complicated plot up so well. Contrary to some critical opinion, they didn't fall back on some cheap and contrived Hollywood trick.
What is most important is the fact that Neo sacrifices himself and makes all his choices voluntarily; of his own free-will. "Why? Why do you continue!?" Smith rages at Neo. "Because I choose to." is Neo's retort. Neo is the Messiah because he sacrifices himself freely for the good of all men, out of love. This is a major part of his character's evolution, though somewhat eased by the fact that Trinity dies. Thus she is a major step for Neo to evolve past. Love is beautiful and amazing, but even more so when that love is for all mankind, and not just one person. That is divine. Thus in the end Neo makes the choice that he couldn't make at the end of Reloaded. (although, it's a good thing he didn't or else we'd still have no solution to the Smith-cancer or the War between man and machine)