The Matrix is suddenly broken into two smaller Matrices by the US Government to avoid Matrix Monopoly.
(One Tough Hologram, TheRob)
War with the machines was actually started as a battle between Duracell and Energizer.
(Sleepy)
The Nebuchadnezzar's signal system stops working when a new recruit installs a sound card on the ship's computer's motherboard, using up the last of the IRQs.
(Chimerasame)
During the films climax, Keanu Reeves finally admits he can't act and storms off the set.
(Fluff)
The red and blue pills are really just nyquil and the whole matrix thing is a really freaky dream due to jello shooters and a bet between Neo and Morpheus on who can eat more raw oysters.
(pink bunny)
Neo wakes up and realizes, it was all a dream. He and Ted go on to have more wacky adventures.
(jayj)
Most of the movie is played at a very slow speed, due to the Matrix's conversion to Java applets.
(Fluff)
Turns out the Pepsi girl is the real villian.
(I'll do it but I ain't gonna like it.)
Everyone finds out that if they stop believing in Microsoft, it will disappear.
(Bloodbond)
The Matrix crashes, thanks to an old DLL left over from Windows 3.1.
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