- The movie starts with the same scene as The Matrix starts - agents coming to get Trinity, but there are some changes which are happening. Yahya Abdul Mateen is playing Agent Smith's role at this moment. We see that Jessica Henwick (named Bugs) is observing this scene and when it doesn't go the same as the start of the 1999 movie, she decides to intervene but gets caught by the agents and it turns out this is some sub-routine program in the matrix. Just as the agents are going to kill her, Yahya rescues her and it turns out he is not an agent, he is a program built from the memories and essence of Morpheus. So he is Morpheus 2.0. Bugs is actually there to save Morpheus and she makes him take the red pill and saves him and we cut to Keanu who is Thomas Anderson who gets an error message on his computer screen that his sub-routine program has crashed.
- Turns out Thomas Anderson is a game developer who released one of the most well received and successful games of all time in 1999 titled "The Matrix", and its 2 sequels "Matrix Reloaded" and "Matrix Revolutions". He started this game studio Deus Machina with his partner played by Jonathan Groff but he ended up believing his game's message of "reality is just a simulation" and tried to commit suicide by jumping off a building at his game awards party to show he could fly but he survived and has to attend regular psychiatry sessions with his analyst played by Neil Patrick Harris. He goes to a coffee shop called Simulatte where he regularly sees Carrie Anne-Moss who is a housewife and mother to 2 kids and is named Tiffany (because her mom liked Audrey Hepburn). It is clear that the character Trinity in the Matrix games is based on his unrequited crush on her, and Agent Smith is based on Jonathan Groff who is all business while Thomas is the creative type. And we see that other characters are based on other people in his real life. NPH prescribes him more pills - all of them blue in color.
- Throughout the movie, we get flashes of scenes from Matrix 1999 as Keanu gets them as well.
- Groff calls Keanu into his office and says "I know your current project is over budget, but our owners - Warner Bros Studios, want us to make a new Matrix game. They will enforce our contracts if we decide not to. What is the harm in returning to the Matrix once more, or more times". This leads to a very meta montage about what should be in a matrix sequel and what audiences want to see.
- Keanu talks to Carrie at the coffee shop and she tells him she feels a connection with him, and she loves motorbikes just like his character Trinity. She isn't a video game person, but "everyone has heard of the Matrix, it was just that grounbreaking"
- Keanu is at his office when the fire alarm goes off, and Morpheus texts him. Keanu sees him in the bathroom and tells him "I coded you, you can't be real" and refuses to take the red pill. Suddenly cops burst in to the building and we get an action scene - in between this, Groff comes out and sees a gun and starts acting weird like Agent Smith. He takes the gun and shoots Keanu who wakes up at his analyst's house who again explains to him how he has been living thinking the matrix is real.
- Just as Keanu is overwhelmed and decides to jump off a roof "Free your mind... its easy, free your mind", Bugs shows up again and tells him to trust her. She takes him to Morpheus and everything is arranged just like the Morpheus scene in 1999, in fact the Morpheus scene is playing on a screen at the same time "i thought after your reaction to our first meeting in the bathroom, i will make things more familiar for you. Nostalgia - the biggest drug of them all". Keanu decides to go with them and NPH shows up in the mirror to tell him he is still dreaming. This time he doesn't listen and we get an action scene in a tokyo bullet train where all passengers get possessed and attack them (its called Swarm mode in the movie). Finally, they get to a mirror and Neo is reborn in the real world. We see that he is a pod with another pod in front of him. Only 2 pods there - the second one is obviously Trinity. A couple of robots take Neo out and take him to the ship NSEMON(?) or something similar. Bugs is the captain - its been 60 years since Neo brokered peace but Neo has only aged 20 years for some reason. Neo is too dependent on the Matrix after this long and they have to log him back in for him to survive. Morpheus and him have a repeat of the Kung fu fight from The Matrix with enough twists to keep it fresh - this fight helps his system kick in and he awakens in the real world ready to see what it has in store.
- There are now robots and "sentients" working with humans. Morpheus 2.0 can actually appear in the real world through some nano-magnetic particles or some movie magic like that. These robots and humans are now settled into a new place named Io. Bugs takes Neo to Io.
- Turns out Neo is a legend, a lot of people are Neo-ologists who study his life. Io is run by Niobe (Jada pinkett smith in old age makeup) and she shows Neo how things have changed since they started working with the sentients. They now grow berries and other stuff in Io. Neo eats a strawberry and remarks that it tastes the same as the simulation. The sentients are working to ensure that. Niobe takes him through a tour of history and what happened to Zion, which she says was a city devoted to war, but Io is devoted to existence and she needs to do anything to keep the peace. She imprisons Neo but Bugs and Morpheus break him out, and Niobe looks like she expected it.
- They decide they have to break out Trinity and log back in to the Matrix but are confronted by Agent Smith (Groff) and some exiles from Merovingian's castle. Smith tells Neo that the Analyst had imprisoned them in some new Matrix code which was almost impossible to break out from. But now that he has broken out, he can't have Neo go to Trinity and risk being discovered as he likes being free. This leads to a redux of the subway fight from Matrix 99 and Neo beats Agent Smith and Merovingian walks away cursing him (Merovingian is a homeless man). Apparently when the analyst built the new matrix, all old programs were purged and Merovingian, Smith and others barely survived the purge through these new identities.
- Neo goes to Tiffany/Trinity but it turns out its a trap by NPH who explains that he asked the overlords to allow him to revive Neo and Trinity because he knew they were the key to solving the energy crisis which happened when people woke up as per the peace agreement. This had led to the robots fighting each other for power. But the analyst realized that Neo and Trinity can't be together as it would destroy the Matrix he built each time they found each other, but they can't be too far apart as it would not generate enough energy. He needed them to be close together without being together which explains the 2 separate pods and the fact that they are in the same simulation but not together. He also uses bullet time to trap Neo while he is delivering this exposition - its like the Architect scene from Matrix reloaded but better. He lets Neo go but warns him that he will be back.
- Back in the real world, Niobe tells Bugs she should not have broken Neo out as now The Analyst wants Neo to be plugged back in so that the energy generation can continue. Niobe is summoned by Sati from Matrix 3 who is all grown up and played by Priyanka Chopra. She has a plan to free Trinity but it will require all of them working together, but the final decision will be Trinity's alone as they can't free an unwilling mind.
- Neo goes to meet the Analyst in the matrix to try and free Trinity’s mind while Bugs, Morpheus and some sentients free her body in the real world. Trinity meets Neo at the Simulatte cafe and her husband and kids walk in and she decides to go with them. Just as Neo is about to be plugged back in to the Matrix by the Analyst and his goons, Trinity looks at her husband and who is saying "tiffany, come with me now" and says "I never liked that name, my name is Trinity". Neo and Trinity meet and the Analyst puts everyone into bullet time and is about to shoot Trinity when Agent Smith shows up and shoots him, but the analyst manages to activate super swarm mode with every resident of the Matrix being part of the swarm - Smith says his goodbyes and see you laters and disappears.
- Then it becomes a zombie movie with the swarm chasing them. It leads to Neo and Trinity on top of a building and running from choppers with Neo dodging bullets and redirecting missiles and stuff. They decide to jump off the building and get stuck in mid-air. Neo says it wasn't him, trinity says it was her. She can fly now, she flies them to safety.
- We see Trinity and Neo wake up in the real world. The team convenes around them, fade to black.
- But then we see the analyst, and his house blows open and Trinity comes flying in and tells him they will free more minds starting now regardless of whether the analyst wants them to or not and both of them fly away with an upbeat song playing and they fly towards the camera and cut to "The Matrix: Resurrections"
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