The film opens with a team of synthients inspecting a modal within The Matrix. The captain of the Mnemosyne, Bugs (Jessica Henwick), goes in and finds herself in a simulation of Trinity being found by the Agents, although it isn’t the same Trinity as before. She goes through the motions of fighting off the Agents, while Bugs follows and observes alongside the Mnemosyne’s operator, Seq (Toby Onwumere). Just as the Agents appear to corner Trinity, Bugs observes that this isn’t what originally happened, and Seq know it’s a trap.

Bugs is then pursued by the Agents, running into an old apartment building. The lead Agent (Yahya Abdul-Mateen II) catches up to her, and they realize they are in the apartment of Thomas Anderson/Neo (Keanu Reeves). Bugs tells the Agent that she knows Neo is alive, despite others believing him to be dead, because she remembers being stuck in a dead-end window-washing job when she witnessed Neo in his true form stepping over the side of a building and not falling, and when he looked at her, it unlocked her mind. The Agent also acknowledges that he had seen codes in windows and mirrors before he realized he was in a simulation, and the Agent reveals himself to be Morpheus. Bugs presents the blue and red pills for Morpheus to make his choice, and he takes the red one. They try to escape through various doors, only for the Agents to be around every corner after them. The two make their exit by jumping out a window.

In The Matrix, Neo is living as Thomas, working for the video game company Deus Machina, where he turned the original story of The Matrix into a successful video game trilogy based on his memories that he perceived as dreams. His coworker Jude (Andrew Caldwell) takes him to the local coffee shop where Neo sees Trinity (Carrie-Anne Moss). He appears to show interest in her, but when Jude approaches her to be Neo’s wingman, they learn she is now known as Tiffany and is married to a guy named Chad (Chad Stahelski) and has two sons, Brandon (Julian Grey) and Donnie (Gaige Chat).

At work, Neo finds an intruder in his game, but they are purged quickly. He is called to meet with his business partner, Smith (Jonathan Groff), a reborn form of his nemesis within The Matrix. Smith tells Neo that their parent company, Warner Bros, wants to make a sequel to the Matrix trilogy, implying that they are being forced to do this. Neo then goes to see his therapist, “The Analyst” (Neil Patrick Harris). They discuss a previous suicide attempt, which was the moment Bugs saw Neo stepping over the side of the building. The Analyst also gives Neo a prescription of the blue pills.

Neo and his teammates meet with their boss, Gwyn de Vere (Christina Ricci), as they all begin work on their next Matrix story. Neo goes day-by-day feeling a sense of deja vu with everyone expressing their interpretations of The Matrix and its themes. Later on, Neo returns to the coffee shop where he talks to Trinity. She mentions having seen her sons play the Matrix video games, and she thought the Trinity character resembled her.

The offices of Deus Machina are being evacuated, but Neo receives a message to go to the bathroom. He meets Morpheus in there, and he offers Neo the red and blue pills. Neo starts to freak out over realizing his dreams were real, but Agents begin to open fire, prompting Morpheus to shoot back. A gunfight ensues, with Smith picking up a gun and yelling out “MR. ANDERSON!” to Neo. After a tense moment where Smith holds Neo at gunpoint, Neo finds himself back in The Analyst’s office. He continues trying to convince Neo that nothing he experienced was real.

At night, Neo gets drunk and prepares to “fly” as he once did, only to be pulled back by Bugs. She tells him that Jude is a sinister program meant to keep an eye on him, and she convinces Neo to follow her. They go through a door that takes them onto a train with Seq, and they proceed until they encounter Morpheus, along with Bugs’ other crew members Lexy (Erendira Ibarra) and Berg (Brian J Smith). They show Neo images from the game, which are just the memories from his original journey with Morpheus in his original form. Bugs tells Neo that 60 years have passed since the war with the machines, and Neo’s true form that the rest of the world sees is that of an elderly man. Neo takes the red pill and sticks his hand through a mirror where The Analyst sees him and starts to panic. While he appears to try and pull Neo through to convince him he’s just having a psychotic break, the crew is attacked by Agents, leading to another gunfight that forces them to run.

The crew runs back onto the train, where the passenger bots are corrupted into “swarm mode” to attack Neo and the others. After the crew fights and kills the bots, Bugs pushes Neo through a small mirror in order for him to be extracted from The Matrix. He wakes up in a slimy pod like before, and he is pulled out by two machines that the Mnemosyne crew uses called Cybebe and Octacles, who are loyal to the humans. As they fly him away, Neo finds Trinity in the other pod. He is flown through the ruins of Zion before being taken to the crew’s sanctuary in Io, where he is hooked up to The Construct.

Morpheus tells Neo that he is going through withdrawals from what The Matrix has been feeding him, with low odds for survival, but Morpheus has confidence in him. Neo is put in a dojo simulation where Morpheus has them spar against each other, with Neo getting knocked down repeatedly until he believes in himself again and uses his power to send Morpheus flying out and destroying the dojo.

Neo reawakens in the sanctuary, where Bugs formally introduces him to the crew, along with their doctor Ellster (Mumbi Maina), who is the granddaughter of Neo’s former ally Captain Roland. When Neo asks about Trinity, Bugs says they don’t quite know yet how to extract her. The crew travels with their pilot Hanno (L. Trey Wilson) to meet with the now elderly Niobe (Jada Pinkett-Smith). She is angry at the crew for going against her orders in looking for Neo, but she is still pleasantly surprised to see him. After dismissing the crew, Niobe talks to Neo about how he gave her hope for a world without war. She introduces him to their head botanist Freya (Telma Hopkins) and digitologist Quillion (Max Mauff) to show that they have advanced past what Zion used to be. Niobe also informs Neo of the Oracle telling them of a new power rising. Until they understand what is really going on, Niobe has Neo kept in a tower for the time being.

The Mnemosyne crew gets Neo from the tower, and they observe Trinity as she is still “Tiffany” in The Matrix. In an attempt to free her, the crew re-enters The Matrix and enters a rundown warehouse. There, they find Smith, who comes with Exiles (rogue programs) that come in snarling at Neo and the crew, including The Merovingian (Lambert Wilson), now reduced to an angry hermit. The crew battles the Exiles, with Neo utilizing his past fighting skills before engaging in a fight with Smith in a lower level of the building. Smith brutally beats Neo and tells him he won’t be a servant to the higher power any longer. Neo regains his strength and sends Smith flying across the room.

Neo eventually locates Trinity. She talks about a dream she had of people chasing them with him riding with her on her Ducati. It is then revealed that the mastermind behind the new power in The Matrix is The Analyst. He succeeded The Architect and used the machines to resurrect Neo and Trinity after their deaths during the previous war. He originally only wanted to bring Neo back, but realized that it would only work with Trinity there with him due to their strong bond. He has created a balance for the two of them to be close, but not too close, so they don’t overpower his system. The Analyst uses a bot to go into swarm mode to fire a bullet at Trinity in slow-motion as a threat to Neo to return to his pod before The Matrix can be rebooted, which Neo attempts to catch, but The Analyst simply removes it before it hits Trinity. Neo has to flee along with the crew.

The crew returns to an infuriated Niobe to prepare for a court martial. Bugs argues with her that she cares little about their goals to free human minds. A bird-like machine, Kujaku, arrives with a message. Niobe brings Neo to meet Sati (Priyanka Chopra), who was originally a little girl exile program he met (in “Revolutions”) that has been shadowing him in The Matrix when he was still Thomas. She says that her father designed the resurrection pods that brought Neo and Trinity back to life. Despite knowing the risks in rescuing Trinity, Niobe agrees to allow the crew to go along with the mission.

The crew carries out the mission, with Morpheus and Bugs working on Trinity’s pod while Neo goes back into The Matrix to find her at the coffee shop. He speaks to The Analyst, saying that if Trinity chooses to leave The Matrix, he must let her go, otherwise Neo will willingly return to his pod, and The Analyst agrees. Trinity arrives and talks to Neo, saying that she played his game and recognized the images as her own memories. Her husband and kids arrive to try and get her out, but Trinity snaps out of it and declares she hates the name Tiffany and is officially Trinity. She and Neo battle the Agents and overpower them once they bond. The Analyst is met by Smith, who fights him after declaring himself free, and he briefly forms an alliance with Neo and Trinity to allow them to escape by shooting The Analyst and temporarily incapacitating him.

Seq detects trouble in The Matrix, so Neo and Trinity ride through the city on her motorcycle, just like in her dream. The Analyst regains power and starts using bots to divebomb down onto the streets to take out the heroes. Neo and Trinity make it to a roof where two choppers fire at them, but Neo uses his power to deflect a missile and take out one chopper. Trinity then tells Neo that she remembers everything about them and their relationship. The two leap off the building together in an attempt to fly, but only Trinity holds that power and hangs onto Neo as they get away. They are extracted and reunited for good.

Neo and Trinity locate The Analyst in his apartment, where Trinity gives him a few good punches for his manipulations. They threaten him if he tries to take control of The Matrix again, and they fly away together to restore balance to The Matrix.

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After their deaths during the previous war with the machines, Neo and Trinity are resurrected by a program called The Analyst, who poses as Neo's therapist in The Matrix. Neo has been living as Thomas Anderson again, now a video game designer who turned the original Matrix trilogy into a game franchise, while Trinity is now Tiffany and is married with two kids. Neo is found by a reborn version of Morpheus and a woman named Bugs, who leads a resistance crew called the Mnemosyne. They pull Neo from The Matrix and convince him that everything he thought was a dream is real.

Neo wants to get Trinity out of The Matrix, but it is complicated by certain risks, such as the crew believing Trinity may prefer to be where she is. Niobe, who is now general of the crew, admonishes them for going against her orders and bringing Neo back, but eventually comes around and agrees to help them save Trinity.

Neo faces off against The Analyst and his Agents in The Matrix, but Agent Smith, who refuses to be under The Analyst's control, forms a brief alliance with Neo to help him and Trinity get out. They manage to escape the villains and are reunited outside of The Matrix once again.

Neo and Trinity threaten The Analyst's life if he should ever interfere and try to control them again, and they head off to restore balance to The Matrix.