@Saikou Barry I'd say that agent Smith is very much to blame. Although, since hes a program he probably isn't wired in the same way as a human. But he's sort of a dark alternate version of Neo. He rejects the rules, and the binary options of one way or another. But rather than try to create a new system, self-delete himself, or position himself as just a observer, his decision is to retain his purpose and defeat Neo, and pretty much break the whole cycle of In matrix/out of matrix into nothingness. So there's a choice as Agent Smith has free will at this point. He chooses to to follow his nature (For lack of a better word in artificial people) in removing problems, it just so happens the problems to him are literally everything now. Thats just my opinon tho!