The Matrix Revolutions
Quick revision to the end of Reloaded. The sentinels still attacked, and were still stopped, but we play it up so it looks like Trinity is responsible for saving them.
We begin Revolutions with a very anxious and nervous Neo, on board the Hammer, hoping they can somehow find Trinity in the Matrix. They get a call from Seraph, and head in. They learn the Oracle has been kidnapped by the Merovingian, so they chase after him, and follow him to the train station. Just as the fight is starting and we start to see what kind of cool stuff the villains can do, Smiths show up, and manage to absorb Seraph. In the fight, Morpheus manages to kill Monica Belucci, which somehow transfers to him all the bits of power she had stolen from previous 'The One's. Now we have three heroes with strange powers. I think we'll give Morpheus a power to have Matrix powers in the real world. Just something to shake things up.
Anyway, things are looking bad in this fight, until, for just a moment, Seraph's personality emerges from Smith, long enough to give Neo and Morpheus time to escape, but capture Trainman (who needs a better name) and are able to rescue Trinity. This scene is necessary to show that sometimes, a strong personality can still persist briefly even after Smithifying.
Trinity stands in for Neo in the earlier train station scenes. She has to learn how things work here, because she will later have to use this wisdom when they go the Machine World. See, we have the real world, and two Matrixes. One Matrix is the one where human minds live, kept placid. The other Matrix is where the machine minds live. The truth is, the Machines do not know how to heal the world, and even they cannot stand to live there normally, so they created a Matrix of their own. Human minds, batteries of creativity, provide the processing power to make the Machine Matrix possible, and, when we finally see what it looks like inside, its like nothing machines could imagine or we could experience. The Machines could not live in a Matrix of their own design, because existence would lose all randomness, and there would be no growth. The truth is, androids do not dream of electric sheep; humans do.
In this version, the Oracle is missing, kidnapped by the Merovingian, who intends to take her and consolidate his power in the Machine World. The Oracle is able to understand human dreams, and so left the Machine World because she could control things there, undoing the necessary improbabilities. The Merovingian, with her in his clutches, will be able to change the world as he desires.
In the Machine World, they still have human bodies, because they were designed to exist in the Matrix, unlike certain special programs, like Agents.
Smith has taken over the entirety of the plugged-in humans, and all the programs that could have fled to the Machine Matrix and severed ties between the two virtual worlds. But Bane, existing in the human world, can bridge the gap, and when Neo and Trinity realize they might be able to stop the machine army by destroying them from within their own Matrix, Bane stows away with them. When they get to the machine city, he waits for them to log in, and then he logs himself in. As Neo and Trinity try to understand this strange, lush world (which we might tint slightly gold), Bane/Smith reopens a passage between the two Matrixes, and his other selfs swarm into this world.
The Machine World falls to Smith too, and the two worlds begin to merge into one. Neo and Trin try to get the remaining machine upper-ups (like the Architect) to call off hostilities with the humans, but they refuse human help.
Now, we get to have cool stuff with Morpheus. He went with Niobe and folks to save the day at Zion. After absorbing some One power from the vampire, guess what he gets to do? Have you seen that ridiculous Star Wars: Clone Wars cartoon episode where Mace Windu sprints around punching robots? Well, Morpheus is cooler, because he'll be punching sentinels off the hovership as he clings to the outside of its hull, while Niobe pilots it toward Zion. I dunno, maybe this is cheesy, but Morpheus deserves something cool.
Our grand climax goes down at a strange hellish/goldish/greenish dual-Matrix realm where the Merovingian is trying to extract power from the Oracle. We have a first fight where Neo and Trinity (and what the heck, Seraph too) try to rescue the Oracle, fighting Merv and Monica. But as we finish that cool fight, an army of Smiths swarm in, each of them trying to just reach the Oracle. They surge past Neo, who's doing crazy stuff to keep them away, and one manages to reach the Oracle and absorb her power.
Then we get a big flying fight like at the end of the current draft of Reloaded. Except in this version, we play with reality. After some initial kung fu, Smith beats Neo up into the sky, and then he starts pulling lightning bolts from the storm, striking at Neo with those. There is some sort of huge explosion that obliterates blocks of buildings, destroying the Smiths in those buildings as well. During this fight, Trinity watches from a rooftop, powerless to help, and as things are looking bad, they get worse, with a few normal Smiths coming at Trinity, surrounding her in a sick reenactment of the opening scene from the first movie. Neo has to save her.
See, this is why the fight at the end of Revolutions stunk. They killed off Trin so Neo'd have nothing worth living for. But he needed something worth fighting for, and he didn't have it. Here, he will.
Something special and nifty happens here. I'm not sure exactly what, but somehow Trinity's state as a higher being comes into play, either as she donates power to Neo, or Neo pulls her away and lets himself get absorbed in her place, or something. But just as Smith is spouting off doomsday proclamations, something cool and unexpected happens. We don't draw out the punching too long, and there are certainly no CG people fighting. When Smith is finally destroyed, billions of Smiths shatter across the world, revealing the humans beneath, or completely obliterating those programs Smith absorbed.
People occasionally ask why God lets the Devil exist. It's the same reason Neo made Smith a virus. So that, ultimately, evil can be defeated. With Smith's destruction, the world is free from the machines, and though the people who survive will have a hard time enduring in the world, they'll manage. We can even still end on a sunrise, but it'll be a real sunrise.
So yes, that was rather eclectic, but hopefully there were some useful ideas.