In real life, 60 years have actually passed since Neo and Trinity flew to Machine City. In The Matrix, the Matrix has been reset several times, and it has been 20 years since the latest reset.
The Real World after 60 years and the Matrix after 20 years
In The Matrix 3, after Neo defeated Smith, a temporary peace is established between the humans of Zion City and the AI Machine Cities. The Matrix was also restarted, and humanity basically continues to live in the biological tank to provide energy for machines, while the soul lives happily in the Matrix.
The Analyst (
Neil Patrick Harris) succeeds and replaces the Architect to become the program master that governs and operates the entire Matrix. The Analyst was the one that managed to save both Neo and Trinity's lives after the events at Machine City, with the aim of studying Neo's body to discover the source of his powers.
He also developes a new code system that can disable Neo's power in the Matrix, to some extent.
When Neo shows signs of recovering old memories, The Analyst acts as a physiotherapist, trying to calm him down and prescribe blue pills - which keep him at peace in the Matrix and erased any memory as it arises.
Neo and Smith in the New Matrix
Neo in his 50s, whose real name is Thomas Anderson, continues to work as a programmer, but now is a game programmer. Based on his dreams, he designs a game also called The Matrix - with all the characters like what happened in the previous Matrix trilogy.
As predestined, Neo is working for a game company owned by Smith (
Jonathan Groff). Smith could not recognize Neo because The Analyst programmed Neo to have a new appearance.
Smith also continues to be an exile program in the Matrix – living out of The Analyst's supervision. Over the past 20 years, Smith has also spent a lot of time researching Neo's martial arts and upgrading himself to nullify it.
In the developments of The Matrix 4, the relationship between Neo and Smith is complicated, sometimes enemies and sometimes reluctant and unexpected allies. Essentially, Smith is grateful to Neo for helping him become exile program but liberal, independent and powerful in the Matrix.
A funny point of interest is the exile program The Merovingian (
Lambert Wilson) - The luxurious, lavish and lustful French gentleman after resets has now become a filthy squalid beggar.
City of Zion to Io
According to the recall of Niobe, after Matrix 3, Morpheus was elected High Chair of Zion's Council and believed that with the peace between humans and the Machine City, Zion would be at peace. However, there was a civil war between the machine cities themselves for energy and Zion became a victim. It seemed that Morpheus and many others died in this war.
The survivors revived Zion and developed it with a new name of Io. Io has built a biological sky in the ground, and now can grow plants and fruits.
Several intelligent machines (called synthients) fled the city of machines to join Zion and became human companions such as Cybebe, Octacles, and Lumin8. In overall, they look like pets to human now.
Captain Niobe (Jada Pinkett Smith) is now in her 80s acting as the powerful General, manage all Io's security operations and ships.