A gargantuan explanation..cut & paste of course. =D

Matrix Theory possibly Explained

Zion is a program, just like the Matrix. How is Neo able to figure out that he is able to stop the sentinels in Zion near the end of the film? The spoon given to him earlier. It had obviously been bent loads, but how outside the Matrix?? This gave Neo the inspiration and the understanding that Zion is still a matrix.

"The One" is a program, but has to be "attached" to someone in the Matrix. So Mr. Anderson got it in the 6th version of the Matrix. Then "The One" program's purpose is to allow Zion to be destroyed then to rebuild it. The reason for this is
because of anomalies - the 1% of humans that don't accept the Matrix.
These are all brought out of the Matrix program and into the Zion program by the
"Morpheus" program and other similar "ship captain" programs. Then
once all the anomalies are out of the Matrix (and in Zion), that is the time for Zion to be destroyed, thus killing all the anomalies off. The Matrix is then upgraded, thus creating the next version of the Matrix, but Zion must be rebuilt so that the next lot of anomalies can be brought out again so that they can be destroyed. This is the feedback-loop, and is the reason to retain a handful of people so that Zion can be rebuilt. So this is why Neo said the prophecy was a lie - the One's purpose was not
to end the war as the prophecy stated.

Unfortunately, "The One" program must be re-used each time, or copied, so it can be "attached" to a new anomaly inside the Matrix. So what happens to the old "The One" program? It faces deletion, and as the Oracle explained, it goes into exile
instead, just like the French bloke (the Merovingian) did. He was the first One(probably from the second version of the Matrix), and once he fulfilled his duty, he became an exile program and "abdicated" his "Oneness" by choosing Persephone and power. This is evident in the bogs when Persephone asks Neo to kiss her. She
says she wants him to kiss her so she can feel what it is like again to be kissed by
something close to human, just like the Merovingian used to be. Then she says to Trinity that she envies her, but that these things are not meant to last. So the Merovingian used to be just like Neo - a One - thus proving further the feedback-loop explained earlier.

The correct door in the Architect's room
Now there are two possibilities here:

1. All the previous One's chose the right door allowing a "temporary dissemination" of their code into the Matrix (i.e., the code they "carry" thus indicating Neo is indeed
human), then he must select (unplug) 23 people from the Matrix to rebuild Zion. This takes away the possibility that stories from previous rebuilds of Zion will be carried
through. But Morpheus indicated in the first Matrix that this is the case anyway. He said, "there was a man born inside, able to change things, it was he who freed the first of us," - basically the One previous to Neo. And this proves that the previous One chose the right door also. Neo's purpose is also to choose the right door, but he does not because he faces deletion afterwards and has the choice of going
into exile - programs choosing to go into exile is the one thing that can't be accounted for in program parameters. Thus, he chooses the left door instead this time. How was Neo able to choose the other door? Because of his extreme willpower? - Even the Architect indicated that he'd noticed this - "Interesting. That was quicker than the others." Or more likely, because the Oracle upgraded his
coding with the candy on the park bench. The candy/cookie was a method to
change the One's program. She said he has made a believer out of
her - this is quite human-like and perhaps the previous One's didn't accept the upgrade candy, now she has hope... hope that Neo will finally choose the other
door.

2. All the previous One's chose the left door, saving Trinity and letting Zion fall. So this time is no different. But the Architect does say, "You are here because Zion is about to be destroyed. Its every living inhabitant terminated, its entire existence
eradicated," and also, "this will be the sixth time we have destroyed it, and we have become exceedingly efficient at it," - assuming the Architect isn't lying, then they
have already destroyed Zion (i.e., Zion has fallen) five times - i.e., the
result of going through the left door.

Morpheus and Trinity are programs. Morpheus's purpose was to find the One and
deliver him to the Architect. Trinity's purpose is to control the One by getting in
love with him. Trinity is supposed to be the mother of the new One every time the Matrix is Reloaded. That's why the sex scene was so important and why she was named Trinity.

The Architect says, "she is going to die, and there is nothing that you can do to stop it." He was correct though because she did die just like Neo did in the first Matrix (Oracle said he or Morpheus would, and she didn't lie, but he came back to
life). Trinity dies, but comes back to life (we are using medical definition of death in
all this of course!).

The Architect has already laid down an ultimatum for Neo choosing the left door:

The Architect - "Failure to comply with this process will result in a cataclysmic system crash killing everyone connected to the matrix, which coupled with the extermination of Zion will ultimately result in the extinction of the entire human race."

Neo - "You won't let it happen, you can't. You need human beings to survive."

The Architect - "There are levels of survival we are prepared to accept. However, the relevant issue is whether or not you are ready to accept the responsibility for the death of every human being in this world."

Looking at this further, the Architect does say "coupled" with the extermination of Zion will the human race be exterminated. So he says everyone connected to the Matrix will die, but if Zion is not exterminated, the human race will not necessarily die. Also, there is likely to be a time-window between not going through the right door, and the cataclysmic crash, thus allowing Neo to unplug as many as possible from the Matrix, then those people won't die. This will be the start of the next Zion. As for the Matrix, a cataclysmic crash doesn't mean the end of the Matrix - just needs rebooting or reloading!

Agent Smith is the only "human" in this world. He's the one spreading himself like a virus replicating himself over and over until the Matrix will finally get overloaded and fail. Smith is the one who wants to get out of the Matrix for good. He said so in the first Matrix, "I must get out of here, I must get free! And in this mind, is the key," squeezing Morpheus's temples, "my key! Once Zion is destroyed, there is no need for me to be here!"Smith knows that by killing Neo he can escape the Matrix because Neo is the key to resetting the Matrix, or to shut it off. It was originally killing Neo (in the first Matrix) that allowed Smith to become powerful (cloning ability) - so killing Neo again will allow him to gain Neo's powers completely, and thus gain the power to shut down the Matrix.

So where the hell did Smith come from if he wants to destroy the Matrix? He's obviously not meant to be there - he's a computer virus as he has every characteristic of a virus -he multiplies and spreads and infects (and emulates) other programs like one. He is exactly as he described humans at the end of the first Matrix - "You move to an area and you multiply and multiply until every natural resource is consumed and the only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus." But who put him there? This will only be revealed in Revolutions(Revelations?) I guess - but I'm betting on humans in
the real real world, i.e., outside of Zion and the Matrix. They're at war with the machines and trying to destroy them by infecting them with this virus - Agent Smith. So the irony with this theory is that Agent Smith represents the human race!! Neo represents the machines! Agent Smith says to Neo just after he's seen the Oracle that he became free when Neo destroyed him in the first Matrix (remember when Neo entered his body and exploded him from inside out) - as a virus, Smith has the ability to "inherit" other programs' abilities and thus inherited some of Neo's.

The anomaly is all the humans that do not accept the Matrix. The Architect says "Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the matrix. You are the eventuality of an anomaly, which despite
my sincerest efforts I have been unable to eliminate from what is otherwise a harmony of mathematical precision. While it remains a burden to sedulously avoid it, it is not unexpected, and thus not beyond a measure of control." This includes Neo, but Neo's Matrix avatar is attached with the One program so that he canfollow his purpose as explained earlier under "The One explained".

However, he is also supposed to protect himself and destroy anything that gets in his way - i.e., Agent Smith - so that he may fulfil his purpose. Further proving Neo - and other non-accepters of the Matrix - are the anomaly, the Architect
says, "Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the matrix." The clue here is Neo's program name - "The One". Take one- third for example. 1 over 3 is 0.33333 recurring. A computer cannot deal with recurring numbers, so must accept a limit, let's say 0.33333 for argument's sake. Multiply by
3, you get 0.99999 - never 1.00000, where has the "remainder" 0.00001 (One) gone? This is the limitation of computers, this is the mathematical imprecision inherent in programming (of the Matrix) and the eventuality of the One anomaly unable to be eliminated.

What is the equation then? Not sure, but it definitely involves pi. The Keymaker refers to the window of time to open the door to the mainframe as 314 seconds. 3.14 is pi to three sig. figs., or the number of radians in half a circle. Half a circle is like the cross-section of a womb, similar to the alcove of Neo and Trinity's love scene - conceiving the next One? "NEO", incidently, is an anagram of "ONE". Trinity and Neo - one on one; a choice - one or one. Leads us to
101. "101" is mentioned numerous times in Matrix 1 and Reloaded. Neo's room at the beginning, Merovingian is on the 101st floor, the 101 freeway of the car chase in Reloaded, then when Trinity is hacking into the power plant system, she resets the password to Z10N0101. Freaky. Indicates that she is a program because that's not some random password she's put in. 101 is binary for 5, which in zero-based binary counting: 000 is 1, 001, is 2, 010 is 3, 011 is 4, 100 is 5,
101 is 6 - And this is the 6th version of the Matrix! Then there's 303. 303 is the room Neo got shot in Matrix 1, the Oracle lives in room 303, it's also the hotel room number Trinity is in in Matrix 1 and it's seen at the end when Neo fights the
Agents and Smith and begins to literally see the code that makes up the Matrix. 101 x 3 = 303, a trilogy, 3 + 0 + 3 = 6 = the 6th Matrix. Trinity means 3.

Who is the "mother" that the Architect refers to?
The Architect says, "Please," in an almost disapproving sense when Neo suggests the Oracle, but does not reveal who
it really is or even directly that Neo is wrong. The architect was the one who created the Matrix; the co-creator is neither
Persephone nor the Oracle. Both of them are only programs that have a purpose in the matrix, just like the rest. The Architect is in charge of the Matrix world and the co-creator is in charge of Zion. She has almost the same age as the Architect. Therefore, that woman is the Head Counsellor, the only woman of importance that lives in Zion and the one who asked for the two captains to volunteer at the council meeting. She's the one who knew all along about the Matrix.
She was the one who told Zion's Defence Minister to cool off and to let Morpheus do his work so things could go as
planned. Or alternatively, it could indeed be the Oracle. She is the only program that truly wants humans to have a free
choice... at the same time, she sees the future, because she knows the program code - she is like God - which is why Seraph protects her - see "Who is Seraph?" below.

What's so special about Neo's avatar?
Neo is a skilled hacker, and his avatar in the Matrix is based on the person that founded the AI of the original machines
that eventually took over the world... How? Take a look at the disc he gave to the bloke at the door at the beginning of Matrix 1. It said "DISC AI" on it. The hollowed book Neo takes the disc out of is "Simulacra and Simulation" - a collection of essays by the French postmodernist philosopher Jean Baudrillard. He opens it to the section "on Nihilism" (meaning nothing is truly known, etc.). "Baudrillard's concept of simulation is the creation of the real through conceptual
or 'mythological' models which have no connection or origin in reality. The model becomes the determinant
of our perception of reality--the real." And Morpheus says, "Welcome to the desert of the real," in Matrix 1. I'd say this book describes The Matrix to a tee. So this disc contains the key to the AI, and thus how to destroy the machines, so I think they'll use this info in Revolutions to ultimately destroy the machines, which means he'll have to go back to the nightclub and find the guy he gave it to.


Who is Seraph?
The reason Seraph (the chink guy Neo meets before meeting the Oracle) had golden code and was so spectacular
is that he came from the first incarnation of the matrix, which was heaven. "Seraph" is singular for the plural "seraphim". The seraphim are the highest choir of angels and included amongst others: Lucifer, Gabriele, Raziel and Malaciah, and they sit on the 8th level of Heaven just one below God. So Seraph will obviously have a big part in Revolutions, but whose side will he be on - the machines or the humans?? That is the question.

The Twins
They are exiled programs that emulate the human myth of ghosts as the Oracle explained. They are programs behaving
badly. Persephone killed one of the Merovingian's bodyguards with a silver bullet because he was emulating a werewolf. So if the Twins could phase into ghost form, why didn't he when his arm was trapped in the door of the garage? Was it because he was wounded or because he can't phase when his arm is trapped? No of course not. The doors of that
building, when shut, always led somewhere else (usually in the mountains) when opened again without the Keymaker's key. So if it were slammed shut due to the Twin phasing into ghost form, the Twin's arm would've ended up god knows where, but certainly not attached to the Twin's body.