Nothing gets on Neo. It was all in his mind.
When he took the red pill It interrupted his input output signal. With that signal being blocked, it would cause him to wake up. Thus alerting the Sentry Guards of his status. Once they has ascertained if he was really awake, they would flush him into the sewers. Once in the sewers the crew could go to the location of the exiting port and pick him up.
Morpheus: This is your last chance. After this, there is no turning back. You take the blue pill - the story ends, you wake up in your bed and believe whatever you want to believe. You take the red pill - you stay in Wonderland and I show you how deep the rabbit-hole goes.
Morpheus: The pill you took is part of a trace program. It's designed to disrupt your input/output carrier signal so we can pinpoint your location.
Neo: What does that mean?
Cypher: It means buckle your seatbelt, Dorothy, 'cause Kansas is going bye-bye.
Neo: Why do my eyes hurt?
Morpheus: You've never used them before.