After Neo chose the red pill and was ejected from The Matrix, a large machine came to unplug him.
Why didn't it kill Neo?
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Sign up to join this communityAs a matter of fact, the Doc Bot did attempt to kill him almost immediately after it unplugged his ports, by flushing him down into a sewer where he would have drowned if there hadn't been a ship waiting for him. This seems to be standard procedure for any body that it reads as having been ejected from the Matrix (see below).
According Taki Kunitake (Head Illustrator for the Matrix) in the The Art of the Matrix book, he states that the Wachowskis intended for the Doc Bot to have read him as a dead body anyway, presumably as a result of the pill that the Rebels gave him to "disrupt [his] input/output carrier signal"
Kunitake: One thing that was really nice in the film, something that wasn't in the storyboards, was the reflection Neo sees of himself on the face of the DocBot. I thought that was a really cool evolution from the boards, tying in to his whole path. When this robot comes down, very threatening. Larry and Andy wanted a bit of a shock, so it reaches out end grabs his throat. As an audience, you're thinking it's going to twist his head off. but it actually disengages. They'd talk about how the DocBot is reading Neo as a dead body, a dead battery, and disengages him so can flush him from the pod. Even in the script, they wanted it to be very graphic: very shocking. I was trying hard to get that sensibility.
Of course, we later learn that the entire Matrix/Zion project was set up to allow humans the illusion of choice. If your only options were to stay in the Matrix (and cause trouble) or to die, the system would break down much sooner. In that sense it makes far less sense to kill escapees than to actually let them escape.
Similar to a previous question about seemingly senseless behavior on the part of the machines, the answer is two-fold:
The docbot is just doing what it's programmed to; in this case, it finds humans that aren't plugged in anymore and disposes of them. It may not even be aware that he's still alive. It's possible that the docbot figures anyone who's "carrier signal" is disrupted must be dead, and just watches for them and throws them out. Or, it might just not care, figuring that if the human's still alive, it will starve to death soon enough.
As for why the docbot is programmed like this, it's because the master plan of the Matrix requires letting humans go. On one level, it has to allow humans to choose to reject the matrix (that's part of the free will requirement that keeps the matrix working). But even beyond that, it relies on the freed humans to build up a settlement and ultimately work towards the return of The One, so the "glitch" caused by all that built-up free will can be purged. So, it's ultimately part of the machine's plan to let humans escape every so often, and killing them would defeat the purpose.
That wasn't a sentinel (the type of machine designed to kill Zion operatives), it was a machine nicknamed the "Docbot".
Sentinel:
Docbot:
Unlike the sentinels, the Docbot's purpose is to monitor humans plugged into the Matrix and eject them if necessary. Machines do not stray from their purpose, so the Docbot did not kill Neo.
In any case, Neo would have died without help from the Nebuchadnezzar since his muscles had atrophied and he would have drowned in the sewer. It would not have been necessary for the Docbot to kill Neo.
I always assumed the rebels had hacked into the Docbot's control systems and ordered it to free Neo. If they can hack the Matrix itself, presumably they can do the same with other systems belonging to the machine civilization.
As other answers have noted, the machines want humans to be able to escape from the Matrix. However, that system requires that the rebel humans have the illusion of choice. They must believe they are heroic rebels who are cleverly defeating the machines' security. The machines may well be allowing them to do this, by leaving back doors in the code or similar.