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in m1 didnt neo come from the fetus fields... true ... then he went into the weird tunnel-slide into a big water pit...... then straight into the neb. correct... but where is the water pit.. and how long is that tunnel thing? and how dont the machines not know about this and like close it off?

the machine read Neo as dead.Then it flushed him down a garbage tube or whatever and the humans got him form somewhere.

so that pill kinda marked his body as "dead" in the real world?

probably as a side effect, yeah.

"it disrupts ur input output"

"..so that we can track you"

It says nothing about him being tagged as dead.

xeous is correct, it is made so that his mind can be removed from the Matrix and put into his body, like a hardline for the rebels. The machines see that he is not sending into the Matrix anymore, so he is dead to them. And of course they are not going to plug up the outlet, because then the one would not be able to be freed...

yah, we dont want our hero to still be plugged

many people still don't realize, after seeing reloaded, that zion is necessary for the survival of the matrix.