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The Janitor is the main and true antagonist of Scrubs. He is J.D.'s arch-nemesis.
He was portrayed by Neil Flynn.
Odd origin as imaginary character
The Janitor meant to be as imaginary character in first season in scrubs to protagonist while every else bypass his existence just only protagonist since Season 2 to final season almost everybody "scrubs" officially recognized existence one by one.
In the first season, the Janitor seems to be acknowledged by other characters; however, these could've been explained as coincidences, or the interacting as being part of J.D.'s imagination. For example, in "My Bad", Elliot seems to acknowledge him when she throws a coffee cup down next to him and sarcastically apologizes. In "My Nickname," the Janitor calls J.D. "Scooter" and later, Dr. Cox refers to J.D. by that name. In "My Way or the Highway," the Janitor gives advice to several patients (recommending surgery) and one even indicates that the Janitor is in the room.
The first time that the Janitor interacts with another major character besides J.D. is in the season two episode "My Karma", in which he blackmails J.D. and Turk. From the beginning of Season 2, Flynn joins the rest of the main cast appearing in the show's extended opening credits, but the credits were changed back due to objections by NBC, who wanted longer episodes instead. Flynn has not been represented in the credits since. However, he was still acknowledged as a main cast member by the producers as of the second season. Since the start of season two, Janitor has had encounters with most of the other regular characters. He has even had an entire episode ("His Story III") devoted mostly to him.