Architect has been overthrown by Neil Patrick Harris "Analyst"; Oracle has disappeared
Analyst has burned down Zion; people now live in new hidden city Io along side machines, now called "sentients"
Rebuilt/Resurrected Neo and Trinity
Neo and Trinity combine for the most power of the Anomaly
Keeping Neo and Trinity alive but separate gets best juice from "coppertops"
Neo is now back in Matrix as a game programmer, with Smith as his "partner", who is also trapped
Sees Trinity, now called Tiffany (who has fake husband and kids )every day but no contact
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Movie starts out with new ship captain "Bugs" looking at Nodal, code Neo "Thomas Anderson" built into his game
Essentially replays opening scene with Trinity but it goes wrong, Agents capture Trinity until Bugs intervenes, who then gets caught by another agent, who is new Morpheus, made by Neo, part Smith, part old Morpheus
Bugs unplugs Agent Morpheus and gets them both out
Neo has sessions with Analyst, keeps seeing scenes from previous movies throughout his day
Analyst gives him Blue pills, while take flashes of Neo as old
Neo finally meets Trinity and shakes her hand, has weird connection when they touch
New Morpheus tries to get Neo out but cops show up and firefight starts, Smith picks up gun and kills Neo, who comes to at Analyst office.
Goes home is going to jump off roof but Bugs shows up and convinces him to take Red pill to save Trinity
Analyst sees Neo through mirror and tries to pull him back through
They walk through portal to train in Japan to try to avoid agents
All of sudden passengers get "Matrix code" eyes and crew yells "Swarm" as passengers go berserk and attack
Bugs and co get Neo out through tiny mirror as Sentient picks Neo up from remote place in machine city, with another pod for trinity
Scene where Neo has to fight to stay alive in real world to kick Blue Pill habit, Kung Fu Dojo fight with New Morpheus
Exposition, where crew explains about new state of world, some good machines, architect overthrow, etc., Analyst not yet revealed.
Neo taken to Io, where they meet Old Niobe, Jada Pinket Smith in a ton of make-up
More Exposition about overthrow, missing Oracle, Morpheus getting killed and Zion Wipeout
Neo imprisoned by Niobe to not risk peace, Bugs breaks him out to go get Trinity
They go and try to break Trinity out, Smith gets in the way, reveals he hates Analyst but has to answer to him, that he can't be free as long as Neo is risk
Smith brings in Merovingian and his exiles, stupid fight breaks out; Morpheus loses to Smith like in first Matrix, Neo beats Smith like in first Matrix
They find Trinity and try to break her out;
Analyst shows up and pulls "Bullet time" where he stops Neo and fires slowmo bullet at Trinity, threatens Neo that if he doesn't come back, Next time he'll kill Trinity.
Io Ship shows up and tells them to come back and face music for breaking Neo out.
Back at Io, Sentient, which turns out to be Sati (little girl program from Revolutions, now grown up) shows up and says there is a limited window to get Trinity due to Analyst's overconfidence
Complicated plan explained as it is executed much like in Revolutions; they get Trinity out of pod via shenanigans but in Matrix she starts to choose fake husband and kids over Neo
Suddenly she has a "My name is Neo" moment and her husband goes Swarm; she starts kicking ass
Analyst pulls Bullet time and get ready to execute her
Suddenly Smith walks in moving at normal speed; starts kicking the Analysts ass
Huge fight breaks out and Trinity and Neo try to reach each other.
They touch and huge explosion seems to win the day
Analyst finally reaches black cat he has been chasing which seems to give him power and he orders full lockdown
Smith shoots Analyst and then announces their little alliance is at an end and mentions he could be anyone or "everyone"
Super Swarm starts coming down the streets in every direction towards crew
They ask Neo if he can fly (running theme in movie) He tries and starts to but still can't.
Trinity and Neo ride off on motorcycle with Neo using One powers to get them out, Swarm closing in
They get to rooftop and it looks bleak, with cops/soldiers all around
They go to jump off roof like in previous moments where Neo flew but he can't fly and starts to fall but she can, and lifts them up to safety.
They awaken on the ship and stare at each other reunited.
Next Scene, Trinity and Neo show up at Analyst's office, blow it up, kick the shit out him, and then they all talk about is going to happen next (what, now are you going to change everything? Yes, we are going change everything. We also wanted to say thanks for a second chance.) It seems they are both flying and have the powers of the One.
End credits
[/Spoilers]