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Major Premise: Neo is a Program. Smith is a Virus.
(Most of you may have thought of this already… in one form or another)
Of course, by now you know, Neo was the most over-hyped anti-virus program every created.
The conniving old girl, the Oracle, used the war with the humans, an eternal play which the machines re-enact over and over for their grim amusement (read Harlan Ellison's "I have no mouth and I must scream"... it's similar :p), as a way to slip the Smith Virus into the Matrix or to modify Smith into a potential virus.
Flashback to Reloaded…
Smith acknowledges that he feels different and that the procession of events in this incarnation is skewed from what he remembers of the last Matrix. (First appearance in the second movie… if you know the exact words, fill them in.) Smith knew he was supposed to die and stay dead until the reset.
Neo should have (in the proper procession of events) killed Smith and gone on to talk to the Architect. It was a given that he would discover his powers against the Agents, and would go on to try to destroy Machine control of the Matrix. It was a given that he would discover his control over this all and face the Architect. At this point, the Architect would give him his choice, and tell him that he was merely programmed to do everything he has done. Properly programmed, Neo would then re-enter the Source, reset the Matrix, and create a new Zion… but he has been de-programmed, through a series of events, hints, and cues planted by the Oracle (one of which would be Trinity)
The final manipulation by the Oracle, the pre-programmed death scene of Trinity, kept him from entering the Source. Without this direct threat to her (remember, he could have saved her as one of the 23 chosen), he could have chosen the other door. The Oracle wants Neo outside of the Source, because he is the only anti-virus for Smith. (Was it in the cookies?)
Neo is not human. He may have started as a Human once, as the ‘real’ one, but he has been cloned seven times. All this crap about Smith/Seraph/Calvin Klein/Michael Jackson being previous Neos does not hold true. We see in the monitors that all the previous Neos were exactly the same. The Architect does not need to bluff Neo by showing false images (flash-forward… “what do you think I am? A human?”), the Architect always tells the truth. Another clue to this is that the Oracle comes “back” after being “killed” in “another shell”. The shell, except for agents, dictates the physical form inside the Matrix. We’ll come back to this later.
Neo is a HUMAN clone. But he is also a program or maybe even part machine (c’mon, Neo controlling/killing machines in the real world WITHOUT machine devices? Get real). Neo’s program ALLOWS him to leave the Matrix with his host. THIS IS IMPORTANT.
We all know Neo’s purpose is to alert the Machines when an optimum level of malcontents in the Matrix has been exceeded. His programming and data analysis subroutines would be interrogated upon his return to the source to allow them to re-program the Matrix. He would then select a few malcontents to reconstruct Zion, and these humans would then scour the New Matrix for more malcontents and free them from it. These humans are unwittingly weeding out their own kind from the general population for destruction.
Being so closely linked or embedded in his human “shell”, Neo would experience the full range of humanity, and would be better able to describe the flaws in the Matrix to his programmers.
Smith, on the other hand, being an Agent, is not en-meshed in the Matrix the way that the Oracle and other programs are. Agents can infect any host they want, and regardless of that host’s original nature, overwrite it. Overwrite, okay, not ABSORB.
The Oracle most likely wrote a subroutine into Neo which would pass some of his powers to Smith. Armed now with the ability to enmesh himself almost completely into his host, like Neo (instead of being just an overlay), he can absorb the knowledge and programming of his host. As a plus, he has Neo’s ability to leave the Matrix inside a host body.
How can we call Neo a program? Simple. He can exist inside the Matrix without a direct connection to his host. An ability he likely “copied” from Smith. The Neo who was left behind on the ship is an empty shell. Conversely, one can argue that the Zion “humans” are ALL PROGRAMS inhabiting human shells, but for simplicity’s sake, let’s say… no.
Now we have Smith as a new and deadly virus created by the Oracle. He remembers that things were different in the previous Matrices. He died six times, and stayed dead. Something is different now. The program is altered. Smith has the power of “The One” over the Matrix and machines (but outside the Matrix, he does not… apparently the power outside resides in the cloned body of the “original” one) and is poised, with the emotional instabilities and psychosis which he inherited from spending too much time in the Matrix, to take over and destroy the Matrix… and after that, the Machine culture.
(Okay, I’ve read some of the posts here already, even if I’m just a noob… cancer, virus, whatever… he’s still an anti-machine Armageddon all by his lonesome.)
(Also note: Neo could still be completely human and be a constructed program. The machines picked up on the original “One” as one who could bend the Matrix… like a program… so it makes sense that he has the abilities and characteristics of one.
Also, Neo's powers outside the Matrix could be explained by: Machine implants, or, more radically, actual power over electromagnetic fields... a biological ability manifested by the first "One", but only rediscovered by the seventh clone.)
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