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According to the Wachowski's, the Red Pill allowed the Nebuchanezzer to find Neo's body in the real world:

"[The Red Pill] is like a computer virus that’s meant to disrupt Neo’s life signal so that they can pinpoint where Neo’s body is in the power plant..." (Source)

In "Kid's Story", the titular character escapes the Matrix by sheer belief that he won't die, but how did the crew in the real world manage to find his body?

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Ship operators can see agents activity on their monitors (I think I remember Link seeing something strange and later concluding that it resembled agents presence). There may be a way to find the physical location of someone being chased by these agents. – Khaloymes Dec 31 '12 at 7:51

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