On Writing Adventures
The first rule of writing adventures for THERE IS NO SPOON is that the more you plan them out, the harder it will be to use Deals and Fates that your players come up with. If you want to use Deals and Fates to their utmost, your adventure slate should be as blank as you can stand. Indeed, Fates and Deals should be used much like Kickers in Ron Edwards' Sorcerer: not just forcing the character into the story, but determining exactly what that story will be about.
If this much improv is difficult for you, the alternative is simply to make characters in advance. Either have your players generate their characters up the week before you play, or bring along some pregens. The middle ground is to design plot skeletons for which it is easy to plug in any Deal or Fate. Some examples of this are in the appendices.
Two simple ways to come up with ideas for a plot is to either steal the plot from another movie and make it fit the Matrix, or simply think about the Matrix and what its existence might imply. The mythical sequels came up with some interesting questions to ask; yours (and their answers) might be completely different. Indeed, you should strive to think outside the box. The key to a good emulative game is maximising the familiar, but still keeping the characters surprised. The former is done here through visual stylings, character play and the rules; your plot elements should thus be bending, breaking and going beyond the "rules" of the Matrix universe, to keep your players guessing. Again, there are some examples of these curve balls in the appendix.
Possibly the best source of inspiration is to remember that the Matrix is a computer program. Look around at the things you do every day, or anything you ever see in a film, and wonder what might happen if you were hacking that level with your Doom compiler. Or turn that idea around and think about all the things your computer does, and wonder how they might look in a virtual world. For example, backing up — presumably the Machines do this. Which means there's a backup of Smith out there. Who — depending on when he was backed up — might not even know Neo exists. Suddenly all sorts of possibilities emerge.
Once you take a story concept and think about it in computer terms, or vice versa, the next trick is to add a dash of spooky-sounding metaphysics. Should you use the backed up Smith, for example, he wouldn't just say he'd been restored from back up. No, he'd declare that he was "back from the dead". He might even allude to Hades, or (since he lost his memory) the river of Lethe. Or, more subtly, have the PCs first meet the returned Smith at the Lethe Corporation complex. Three security dogs prowl the foyer, and a humourless bodyguard will offer to ferry them to their destination — for a price. Although you could then go off and re-tell the tale of Orpheus, you don't need to — just a few hints are all it takes to set the mood. Let the players try and work out which of them was supposed to symbolise Orpheus when the movie is over — that's the effect you want.
Since Matrix stories need no hook (as it is mission based) and have a standard set of narrative elements, they are fairly easy to write. The only problem with them is that, unlike most other stories, the characters (both PC and NPC) have fairly limitless resources and little concern for possessions. Any amount of money or any type of goods can theoretically be programmed in for them. Thus, the only thing that an NPC might want of them has to be something they can do, or something they know. In other words, any time the NPCs can't or don't want to take the characters by force and interrogate them, they can only desire to trade in information or favours, not money or goods. Since being sent on a side-quest can seriously slow down a game, you should take care with any situations that require some sort of commerce or trading.
Ultimately, the only commodity that really matters in the Matrix is faith. Of course, bodies can only take so much kung-fu, and information about Zion is precious, so both of these make good macguffins to drive plot, but the heart of any good Matrix story should involve the currency of faith. That is, not just dealing with what people believe in and care about, but what they do with their beliefs and what they are prepared to risk for those they love.
Neo comes to believe in himself because Morpheus risks so much for him. It is his sacrifice that shows his faith in Neo, and it is that faith that drives Neo to go back and rescue him — a sacrifice repaid, and the circle complete, as Morpheus leaps into Neo's arms. When the helicopter falls out of the sky and Neo, without thinking, tries to hold it up with his bare hands, it's because he loves Trinity. And it is that love that gives her the ability to admit her own feelings, and that's what brings him back from the dead, and allows him to become The One. And it is Cypher's frustrated desire for Trinity, and Smith's frustrated desire for freedom, that drive their evil acts.
And it's all this that makes the Matrix just a bit more than kung-fu against robots.
Go, then, and do likewise.