Apparently Matrix Fans
The reason why the movie made no freakin’ sense is because the big holes in the plot are filled in by the video game.
The brothers’ production scheme was as audacious as their narrative vision: two films shot as one, and more than two years in the making of the real (sound stage) and virtual (computer-generated) elements. They also planned a DVD package called Animatrix —nine short computer films by top Japanese and American anime directors, elaborating on the trilogy’s themes and subplots (it hits stores next month)—and a nifty video game, Enter The Matrix.
For what it’s worth the game looks really cool, but what a rip off.
Update: Check out Animatrix.