What happened to humans that were still stuck in the Matrix?

In the end they have peace. But what are the terms? The machines need the bodies for energy. Are they going to set everybody free and "survive" with low energy levels (the architect said it was possible, although he hints that it would be a somewhat poor existence for the machines...)?

It's a fair question...but understand that most humans won't want to leave. The Red Pills can't just try to free everyone at once - it would never succeed. Far more people would be killed than they could ever hope to save.

Terms of the "new" agreement are that Zion will NOT be eradicated and the people who DO want out can be freed without consequences or potentially being murdered during the attempt.

It seems implied that the reverse is also in effect for deleted programs that want to get IN to the Matrix - no more Exiles. This is why the Merovingian was opposed to the paradigm shift. He loses a lot of influence as the sole point of entry into the simulation for programs.

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I doubt a huge amount of people, enough to fill big cities, would want to know and accept the truth... let alone go seek for it. Therefore I would also say the majority of those already living in The Matrix will remain in their world.

And as it was pointed out, if most of the population decided to leave (be it all at once or gradually over the years), keeping them in the already overpopulated Zion would be... be quite messy. And to reiterate, many would not be able to handle the truth.

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Obviously, they were freed.

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