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i asked some questions a while back, here are some answers if you don’t care about spoilers:

So how did we get from a truce with the machines at the end of Revolutions, to these freed characters back in the Matrix? Some free wheeling conjecture:

• It never happened, it was a joint adventure planned by the machines to give a group of humans some adventure, satisfaction. At the end of this they were all reprogrammed just like Cypher stating, I don’t want to remember nothing! This would raise some questions Imo. [SPOILER="Plot"]It did happen! Neo and Trinity died, and were rebuilt as flesh and blood replicas of themself, then reinserted into the Matrix. [/SPOILER]
• Maybe Neo and Trinity are both manipulated AI and  their adventure from the original trilogy was the equivalent of a vacation? [SPOILER="Plot"]Answer: No.[/SPOILER]
• Is Neo the threat he was in the original series? I’ll vote yes. [SPOILER="Plot"]Answer: Yes, but a poorly articulated threat in the entry. [/SPOILER]
• If so, why would the machines keep him plugged in, why not destroy him? [SPOILER="Plot"]The Architect wanted both Neo and Trinity in close proximity to one another, with the inexplicable reason that “conflict” ups power generation from their human batteries, yet Neo and Trinity are spending their time living pedestrian lives close to one another but zero conflict on their part until the resistance shows up. Maybe the Architect was planning on this to increase power levels, and thought he could handle the situation?[/SPOILER]
• Maybe the machines don’t realize there is a threat, the escape the Matrix fantasy was just another simulation. [SPOILER="Plot"]Answer: No.[/SPOILER]
• How many Matrixes might there be? Not addressed.
• The premise of the original trilogy is that there is a resistance of humans who have escaped  living in the real world. What if there is no resistance, ie humans who have escaped the power generation fields? [SPOILER="Plot"]There is a resistance, there is another underground city. [/SPOILER]
• Less likely: The original trilogy happened but the characters decided that life sucks on a destroyed Earth, so why not volunteer to live the illusion of the Matrix? The problem here is that I doubt Neo and Trinity would volunteer to forget about each other. Yet if you remember the past, how satisfied would you be living in a simulation? Maybe satisfied enough. [SPOILER="Plot"]The answer is No, they did not volunteer to forget their lives and be reinserted into the Matrix.[/SPOILER]