Through a series of links on LiveJournal, I came across this short bit of "Matrix Fanfic" written by Neil Gaiman: Goliath

I find the thought of someone like Gaiman doing Matrix fanfic kind of amusing, but I can't really laugh at it, because it's really damn good. And not just in that "I like Gaiman so everything he writes I blindly like" sense, either. I do love his work, yes. But I like plenty of writers, and while I gush about the stuff I really enjoy, I just don't bother with talking about the stuff I don't like. So while I admit to being a fan-boy where NG is concerned, I truly believe that if you liked the first Matrix movie at all, you'll enjoy this story. Bonus points if you can guess the identity of the antagonist(s).

(When I say "enjoyed the first movie", I mean that this story was clearly written for the whatisthematrix.warnerbros.com website, which was first put together to promote the second film. There's nothing about it that places it in any particular part of the timeline of any of the three movies, but I'm pretty sure that Mr. Gaiman wrote it before the second film was released, that's all.)