A young woman named Bugs learns that the Matrix is running old code in a loop, enacting the moment when Trinity first found Neo within the Matrix.[a] Bugs discovers a program embodying Morpheus and helps free him from the simulation.
Thomas Anderson is the creator of a video game series called The Matrix, based on his faint memories as Neo. At a coffee shop, he regularly encounters Tiffany, a married mother with no recollection of her past, on whom Anderson based the game character Trinity. Anderson has created a simulation called a Modal to develop game characters. He struggles to separate perceived reality from dreams, a known concern among his co-workers and partner. Thomas's psychoanalyst prescribes him blue pills that he takes each day to suppress the occurrences, but he stops taking them. Meanwhile, as Bugs and Morpheus work to extract Neo from the Matrix, Anderson's business partner regains his memories as Agent Smith, Neo's former nemesis.
Neo awakens in a pod and notices Trinity confined in another nearby, before being extracted to Bugs's hovercraft Mnemosyne. Neo is brought to the human city Io, where he reunites with an elderly Niobe. She explains that sixty years have passed in the real world since the Machine War ended, and that Neo's allies, including the original Morpheus, have died over time. The peace achieved by Neo's sacrifice lasted for many years, but the large number of humans leaving the Matrix created a serious power shortage, causing the machines to fight over limited resources. Soon afterward, Zion was targeted in an attempt to get humans to use as the power supply once more. However, this attempt caused many machines, who still remembered Neo's sacrifice and the promise of peace, to turn on the others in order to protect the humans. This allowed most of Zion's citizens to escape. Io was then founded by both machines and humans who have been working together ever since against the remaining machines who want to return things to the way they were before the war.
Niobe refuses to risk Io's safety to help Neo free Trinity and confines him to his quarters. Bugs and her crewmates free Neo and enter the Matrix to contact Trinity. They are attacked by Smith and other exiled programs, including the Merovingian, but Neo and the Mnemosyne crew defeat them as Neo's abilities return. The group leaves and locates Trinity, but before Neo can talk to her, his therapist appears and immobilizes him by manipulating time. He reveals that he is The Analyst, a program designed to study the human psyche.
The Analyst explains that after Neo's and Trinity's deaths, he wanted to study Neo's body and his anomalous powers as The One and convinced his superiors to resurrect both of them. He discovered that due to The One's inherent connection to all humanity in the Matrix, manipulating Neo could make the Matrix produce more energy. Moreover, he found that the code anomaly in Neo was shared in his bond with Trinity, and that by suppressing their memories and keeping them close but always apart, the Matrix generated much more energy. Solving the energy crisis put The Analyst in a position to seize power from The Architect, after which he rebuilt the Matrix to control humans with emotional manipulation, claiming that humans generally believe what they want to believe. Neo's liberation destabilized the system and triggered a fail-safe to reboot the Matrix, but The Analyst stalled the reboot by convincing his superiors that threatening to kill Trinity would coerce Neo to return to his pod.
Neo and Bugs return to Io and talk to Sati, an exiled program that Neo previously met.[b] Seeking to avenge her parents' deaths at the hands of the machines, Sati helps devise a plan to free Trinity. Back in the Matrix, Neo makes a deal with The Analyst: he will return to his pod if he fails to convince Trinity to leave the Matrix. Tiffany reaffirms her identity as Trinity while talking with Neo. Realizing that he has lost, The Analyst attempts to kill her, but Agent Smith appears and attacks The Analyst, seeking revenge for his own imprisonment.
Neo, Trinity, and the others escape in their vehicles, chased through the streets by hordes of bot programs and attack helicopters. As the last ones to be extracted from The Matrix, Neo and Trinity become cornered atop a skyscraper. Holding hands, they leap off and Trinity begins to fly, taking them to safety. With Trinity's newfound control over the Matrix, both return to confront The Analyst. They thank him for giving them a second chance by resurrecting them while they also express their contempt. Neo and Trinity fly off into the sky together, making plans to remake The Matrix.
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