The Ending, explained.

Rating: 9/10 (7 November 2003)

Ladies and gentlemen, the Matrix had a virus. Agent Smith.
The Oracle (the all-knowing, undisputed representative of the humans) made a deal with the Architect (the representation of the monstrous Heart of Machine City):
She would get Neo to eradicate the virus from the Matrix in exchange for one thing: Peace between humans and the machines.
It's a self-fulfilling prophecy, centered around the concept of choice. If Neo hadn't made his decisions, none of this would have happened. Specifically, he's the cause and the cure of the virus (as explained in Reloaded). Smith identified his Purpose in all three movies: he wants out and he wants everything. Period.
Morpheus gave Neo the choice at the very beginning with the Red and Blue pills: eiher wake up now or down the Rabbit Hole.
In the end, even the Matrix itself had made a choice. Everyone did. The results of their choices had consequences. From the first humans who "scorched the sky", to Morpheus who chose to believe against all logic and sense, to Smith who refused to die, to the Oracle who simply yet profoundly gambled that humans would make the right *combination* of choices to produce a desirable outcome for everyone, if given the chance.
Well-done to the Wachowski Brothers for raising the bar for Sci-Fi movies. This is truly a masterpiece. 10/10

ElJay Williams