The Matrix 4 Prequel/Sequel
Many years have passed agent Smith have made it out of the Matrix and into the Machine city. (When Neo destroyed all the copies of Smith, Train man/Smith manage to make it back to the in between world train station. He also learned the best way to make it to the Machine city is incogNEO, like when he did it with Bane.) As he is taking over the Machine world an order of human harvest came in.
A long time ago these same being were the one who seeded the earth. The human race did not progress fast enough to their liking, with the vast different verity they needed. So at some point in time they abducted humans. These humans were implanted with the knowledge to create AI, which lead to B166ER and ultimate to the Matrix.
A huge alien mother ship hovers above the earth as a fading sun is about to rise over the Machine city for the last time. The alien sent down a signal to the Machine city to have their order filled. (The human harvest will be used for food, art, and or clothing, etc…that's a different story, or a different version of Jupiter Ascending.)
Smith was compelled to disobey a direct order from his master creator. Every simulation scenario he played he losses. Then the Oracle/Smith said "The only way for us to get there is together". Smith is reluctant to join forces with the human but do so anyway. What Smith does not realized it that the more program he absorbed the more goodness of Neo he takes in as a by product.
The so called freed human in Zion city are not freed. They are yet still asleep in another level of the Matrix. Smith and Zion joined forces and sent up all the freed humans as harvest with Neo genetic program imbedded.
The human army woke up in the alien ship, with all kinds of super hero like superpower and kicked alien ass. To make a long battle scene short, the joint army won.
All the goodness of Neo Smith absorbed have changed him. Smith stills an asshole none the less. Now a new urge is driving Smith, instead of rampant chaos destruction of the human race, the new agents hungers for knowledge.
A new deal was struck the human keeps the Earth, while Smith and all his AI takes the ship to explore the universe. Agent Smith turned out to be the ONE… The End…
Ops….an alien woke up from the new Matrix pod inside the ship…..