Some folks might not want to even consider that this might be true, but it’s a good point to bring up since it does change the perspective of the story a bit and does fall into line with everything we’ve been told about the Matrix and The One. While it’s true that Neo still has a part to play in the movie that’s extremely important, it’s possible that his role was meant to act as a catalyst to that of Agent Smith, who ended up taking over the Matrix at one point. The signs are all there to be certain since it’s already been explained in a few ways with the same core belief, that The One was born inside the Matrix, and could manipulate the code and so on and so forth. But again, technically speaking, Neo wasn’t born IN the Matrix, he was born in one of the pods that are used to power the Matrix, so he was hooked in from the moment he was birthed, but he wasn’t technically inside the Matrix. It would be interesting to figure out his lineage to be honest, but apparently, the Wachowski’s weren’t going to dig that deep.
But taking a look at Agent Smith, he technically was ‘born’ in the Matrix since he was code created within the system, as he even calls the Oracle “mom”. Obviously, relationships in the Matrix between programs aren’t always given the same level of attachment that humans are used to, but the fact is that Smith was born in the system, he’s part of the system, and once Neo set him free, much as Morpheus was preaching to Neo, Smith was able to go anywhere and do whatever he wanted, as he even managed to replicate his own code and send it into the human world via an actual human. Imagine how strange that must have been before the program, to walk with human legs and actually take in the polluted air of the world outside the machine.
The theory continues to hold up since Smith could have taken the Matrix over if not for the timely rescue measure that Neo initiated when plugging into the Machine City in order to eradicate Smith. It’s very easy to state that Smith didn’t exactly act like the savior that The One is meant to be, but there’s a reason for that as well. The Architect made it known when discussing the future of Zion with Neo that the city had been razed several times, and each time it would appear, thanks to Smith’s rant to Morpheus, that he might have missed out on his chance to get free of the Matrix, as he wished to do. Smith felt trapped within the system that he served and was ready to break free and do this own thing, and it’s very likely that this drove him to be the maddened, frustrated program that he became. In short, he wanted out of his own bonds and might have been very different in the beginning, but by the time Neo finally started coming around to the idea that he might be The One, Smith was already unhinged and bound to take things to an extreme that he hadn’t initially considered.
There’s another part to add to this theory, and it might upset some folks since it might malign a few characters that they don’t want to see spoken badly of, but oh well. One has to imagine that the Oracle is not a saint, nor is she bound to look down upon every creation that has ever come from the Matrix, since as the ‘mother’ of the Matrix she’s bound to be at least somewhat protective of her subordinate programs, though it’s also fair to say that some might have tested her patience a little too much. Smith would have eventually become one of these since his continuing madness would have eventually made him sloppy, cruel, and even a little unhinged until finally, he saw fit to lash out at anyone and everyone that stood in the way of getting what he thought was his, no matter who they were. It does feel that there was regret in the Oracle’s voice when she called Smith a bastard in the third movie, and perhaps a bit of vindication in Smith’s voice when he responded to her. It is interesting to think that if Smith had reached his goal in the first place that he might not have turned out the way he was by the end. If he’d been able to break free of the Matrix the first time that Zion was destroyed, perhaps he would have been able to embrace his full destiny and become someone very different, thereby negating the need for Neo to ever awaken. But then again, it’s a theory, so there’s no telling if this has any bearing on what the Wachowski’s were thinking about.