If you want to know how the interesting setup and hints at a backstory from the second film play out as the story concludes... go hash it out with a few friends in a bar, because you certainly won't learn from this movie.
Which isn't necessarily to say that the backstory doesn't exist... maybe the first draft of the script was a marvelously deft, multi-layered exploration of the nature of reality and artifice, and the human condition. But if so, then in the end they chucked all that stuff to make room for the long, predictable, tedious combat sequences which were vitally necessary to justify their budget. All that's left of the backstory, if it were ever there in the first place, is one interesting scene near the beginning of the movie where Neo has a brief chat with a couple of programs, and a more enigmatic exchange towards the end between the Architect and the Oracle. The rest is mayhem, leaving the resulting film with about the intellectual heft of a Sinbad the Sailor movie -- and as I've not seen very many of those, that may be unfair to Sinbad.