OK, I’m looking back at my past theories and I’m changing things. The machine face in 01 is called Deus Ex Machina, and I think it’s the Source. I always liked to use the Norton Antivirus analogy, but that doesn’t work anymore. See, the gold code is representative of Machine-World language and the green code is Matrix Program Language. This is why the agents are green in the original Matrix movie, and Seraph and the Oracle (presumably) are gold. Gold is sort of the Matrix’s binary language and the green is hexadecimal. That’s the best analogy I can come up with, and since Neo is the One, he can see the Sentinels Operating System so to speak and shut them down remotely. I’m not sure if all the food he was given in any way altered his code or not, but it seems too coincidental that the Merovingian would have included it in his speech on causality if it wasn’t. So when the Source (Deus Ex Machina) plugged Neo into the Matrix at the end, it was able to disseminate the code he carried and reload the Matrix. But wait, what about Smith? When he was erased by Neo, some part of his code was overwritten by Neo so that he carries a part of the One’s code. So when Neo submits to Smith, the Source now has complete access to the necessary code and reloads the Matrix, effectively eradicating the Smith virus.