Within an isolated node of the Matrix, Bugs, the captain of the Mnemosyne, encounters a program running old code involving Trinity's discovery of Neo's location before Agents of the Matrix find her. Bugs finds one of the agents behaving strangely and discovers he is actually the embodiment of Morpheus and helps to free him from the node before it is erased. Thomas Anderson is a successful game developer, having created a trilogy of games based on his dreams of the Matrix, with the aid of his business partner Smith. He frequents a nearby coffee shop where he continues to encounter Tiffany, a married mother that reminds him of his dreams of Trinity. He has trouble separating dreams from reality, but his therapist consults him and provides him blue pills to help keep his sanity, though he later refuses to take it. He notices an intruder in one of his private instances of the game, but later finds that the instance had been deleted by Smith. Outside the Matrix, Bugs and Morpheus discover Neo's signal within the Matrix, despite the belief he had died. They connect Neo to Anderson, and realize he had been unconsciously running the node to allow Morpheus to be found. Bugs and her allies enter the Matrix to help locate Neo's body in the real world, and discover that Smith is Agent Smith, having been keeping close watch over Anderson's activities. Bugs helps Anderson to elude Smith and his new ability to take control over numerous individuals within the Matrix as a swarm. Bugs and Morpheus explain to Anderson what the Matrix is, and with his perception of reality already waning, Anderson agrees to be extracted. Neo wakes up in a pod, finding that a nearby pod contains Trinity, but machine entities, loyal to Bugs, recover him before he can free her. He is taken to the Mnemosyne and to the new human sanctuary of Io, where he is reintroduced to an elderly Niobe. Niobe explains sixty years had passed in the real world since the end of the Machine War, and the human survivors have allied with the machines to keep the system working against an Anomaly within it. Niobe takes Neo to meet Sati, an exile program he had previously met, who explains that the Anomaly was created after the Machine War and had somehow resurrected Neo and Trinity and kept them isolated from others. Though Neo wants to rescue Trinity, Sati warns that there could be consequences of this. Niobe orders Neo to remain outside the Matrix, but Bugs and others agree to defy her orders to try to help free Trinity. Coordinating activities in and outside the Matrix, Neo and Bugs enter the Matrix but are met by Smith and other exile programs would want to see the Matrix returned to its former self. While Bugs and her crew fight the Exiles, Neo faces against Smith, slowly recalling his previous abilities to bend the rules of reality within the Matrix. With Smith defeated, they take Neo to Tiffany's repair shop, but before Neo can talk to her, his therapist appears and slows down time. The therapist reveals himself to be the Analyst, a program that studies the human psyche but has since grown more powerful. He saw Neo and Trinity die at the end of the Machine War but created the resurrection pods as to study them more. Over countless iterations, he found that individually, the two were not special but when they worked as one, they had overpowered the system. Thus, the Analyst has been controlling the latest iteration of the Matrix as to keep the two near each other but preventing them from becoming close. As this has destabilized the Anomaly, the machines have prepared to reboot the Matrix again, but the Analyst has placed that on hold. He threatens to kill Trinity if Neo does not return to be reinserted in his pod. Neo and Bugs are forced to leave the Matrix when another ship loyal to Niobe brings the Mnemosyne back to Io. Neo pleads to Niobe to let him return to try to free Trinity again, and she eventually agrees. Within the Matrix, the Analyst invites Neo to a challenge, that if Trinity volunteers to go free of the Matrix, Neo can take her, but if she refuses, Neo will permanently return to the Matrix; Neo agrees. Trinity, as Tiffany, is brought to them and when the question is posed to her, her family appears. She initially seems to want to go with them, but soon rejects that reality and recognizes that she is Trinity. The Analyst prepare to kill them before Smith interferes, temporarily stopping the Analyst and giving time for Neo, Trinity, and the others to escape. Neo and Trinity race ahead to give Bugs and the others time to extract themselves, but the Analyst turns a swarm of controlled humans against them. The pair race into a skyscraper, and with nowhere else to go, the two jump with Neo expecting to be able to fly them away. Instead, Trinity has come to learn to fly and the two escape and regain control of the Matrix. In the aftermath, Neo and Trinity return to face the Analyst, assuring him that he will face dire consequences should he try to seize control of the Matrix again. Neo and Trinity both fly away to redesign the Matrix.