Basically, what we learned is that the Architect built The Matrix. He built the FIRST Matrix as a perfect utopian paradise... and humans rejected it because we're, by nature, imperfect, flawed creatures -- because we require CHOICE. So there was a specific program created to analyze and understand human behavior -- what we know as the Oracle -- and she determined that humans would 99% accept the Matrix as long as they had a choice in the matter, even if the choice was at a deep subconscious level. HOWEVER, by programming this ability for choice into the system, it created an inherently imperfect subroutine -- since choice cannot accurately be predicted -- and that rounding error of sorts is what's called a "systemic anomaly," or The One. So the 1% of humans who reject The Matrix end up forming Zion and luring more people out of the Matrix, however -- this is a repeating process so Zion has been formed, and The One found, FIVE TIMES already. The machines have destroyed Zion and The One the same five times and have become "exceedingly good at it." So now the Architect gave Neo the choice -- continue with that recursive causality loop (i.e. Zion would be destroyed but the human race would continue), or save Trinity and confine the human race to extinction.