The movie starts off mostly the same as Matrix 1 and Neo is freed into the real world. Neo becomes the one rather quickly compared to the original movie though. As Neo learns of the real world he begins to believe the matrix is better for humanity. Neo tries to convince the real humans to rejoin the Matrix and offers them anyway back in. In response though and amid growing tensions, the leaders of Zion release a virus they had been working on and leak it into the matrix. The virus causes humans to start rejecting the matrix in high numbers and waking up. Neo sees the way humans are reacting to being woken up so early when they aren't truly ready and also the way people in Zion live and he decides he needs to do something so he seeks the machines out.

The machines are freaking out because they can't seem to stop the virus. Neo with his powers realizes the only way to stop the virus is to get people to willingly accept the matrix from within the matrix so their minds stay locked into the matrix. To get this to happen Neo comes up a vaccine in the matrix that is marketed to everyone in a way that allows them choice and because it's obvious that the machines are lying to humans about the virus by willingly taking the vaccine against the virus it tricks people's minds into staying locked into the matrix. The humans who take the vaccine are convinced they are saving humanity and that people who don't get vaccinated are destroying humanity. At first it works but then the vaccines stop working and it's realized humans must take this vaccine every 3 months or they'll wake up from the matrix. Unfortunately though, the vaccines can only be created by The One because they use a special technology that only The One truly has the capability to create. This means the machines need Neo alive forever because they can't produce the vaccines without him at least until they figure out how to to create the vaccine themselves.

Word leaks that Zion begins developing a variant of the virus that will break through the vaccines so Neo teams up with the machines to destroy Zion and stop the variant. The leak of the variant was a trap to lure Neo because in actuality the virus was for Neo not for the people in the matrix. The virus had to reach Neo's real body and couldn't infect him through the matrix. No one knows if the virus will work though. Neo and the machines are succesful in wiping out most of the real humans except for a small group that escapes before they can release the variant into the matrix (though that was never the intention anyway). Neo is infected with the virus without him knowing as was always intended but no one knows if it will actually work. It appears to do nothing and the humans feel defeated.

Neo makes a deal with the machines to leave the remaining humans in the real world alive. Their technology was destroyed and they can't create any new viruses or anything so they're no longer s threat. In exchange Neo vows to find a way to get the machines to be able to create the vaccine on their own because Neo doesn't want anyone waking up from the Matrix again.

Time fast forwards a couple years in the ending clip. Neo is at a vaccination clinic in the matrix and having a discussion with an agent who seems peturbed that Neo is at the vaccination clinic and not researching manufacturing techniques. Neo says he does this to help clear his mind and that he believes he's only a couple months away from coming up with a manufacturing technique the machines can copy. The agent pesters Neo some more about how he's been saying that for months but appear to back off a little. Neo reassures him but that it is tricky. The agent leaves as Neo begins giving a human their quarterly vaccine shot. He asks the person taking the vaccine if they ever thought about what would happen if they didn't take the shot. The person replies that they'd potentially catch the virus and die. He says something like but what if that wasn't the truth? The person laughs and says but of course that's the truth. Neo says "whose truth?" And the person innocently replies that there is only 1 truth. He finishes giving the person their shot and then the camera pans in a manner as the guy walks out where you can see a full vaccine dose in a bottle and an empty saline bottle. Movie ends.