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Help- I re-watched Matrix one last night...
Couple of questions:

1. When neo is "unplugged" otr woken up- why does the machine unplug him? Is it Tank hacking into the system?
2. Once unplugged- couldn't Neo have gone back into the Matrix (as he done several times)- and live his life there- or do the agents automatically detect when they are inserted?
3. If Cypher had not gotten killed off- what would have been the next sequence? He would have killed all the others and been the only human on the ship- My guess is the agents would have to return him to his pod.

1) When Neo awakes in his pod he is now useless or considered dead by the machines. That's why his connectors popped and the machine unplugged him, he was to be liquified(sic?) for food.
2) Note, the agents have already spoken with Neo..er.... Mister Anderson and bugged him. They know he's been searching for Morpheus and probably discovered the bug had been removed. The real question is how could Neo go back? He was pursued by federal "agents" in his workplace after getting chewed out by his boss, which means no more job. Not only that but if you were to find out that your mother is not really your mother, your relationship with her changes a bit. Neo knowing what he knows couldn't have possibly gone back and lived like everything is normal he doesn't like the idea of not being in control of his life.
3) Everybody dies. Agents dispatch the sentinels to take apart the Neb and Cypher gets screwed.

May not be worth much but it's still my two testicles

I think there is a major flaw in the movie.
The machine which unplugs neo can also check to make sure his dead...
It can simply snap his neck... Or do other things to kill him...
But it doesn't...

Then machines don't mind people unplugged that much, do they?