One of Scrubs' most memorable characters, the Janitor, has his true identity kept somewhat vague throughout its nine-season run - and this theory posits that the reason is that Neil Flynn is actually playing himself on the show. Introduced in Scrubs' very first episode as something of a comic antagonist for J.D., the Janitor quickly became a staple of the show and an integral part of some of its funniest moments. His intense dislike of J.D. provided one of the show's best running jokes, and it also saw him regularly bond with John C. McGinley's Dr. Cox, J.D.'s reluctant mentor.
Despite Scrubs' Janitor originally being conceived as imaginary - in early episodes, he's only seen interacting with J.D. - his breakout success earned him a permanent place among the show's cast. From there, one of Scrubs' biggest mysteries evolved: just who is the Janitor when he's not at the hospital. Thanks in large part to Neil Flynn's bizarre and hilarious improvisations, the character was given a complicated and contradictory backstory which only served to further the mystery surrounding his enigma of a character.
It may seem implausible, but the idea that Neil Flynn was actually playing himself on Scrubs is linked to the few glimpses the show gives into the character's past. These either directly link up with Neil Flynn's own past in some way or act as references to other real-life TV shows or events, making the character's identity particularly hard to pin down. The Janitor was one of Scrubs' best side characters, but eight seasons of mystery is hard to dispel, giving way to a theory as mind-bending as the character himself.
The Janitor's Acting Career References Neil Flynn's Own Past
One of the first genuine clues to Scrubs' Janitor having a tangible past within the show comes in season 3, episode 8 "My Friend the Doctor". J.D. spots a man who looks remarkably like the Janitor while watching The Fugitive and attempts to prove that the Janitor once pursued a career in acting before his employment at Sacred Heart. The story is built around one of Neil Flynn's actual career credits - he did appear in The Fugitive in a minor role, which is the first time that Scrubs blurs the lines between the Janitor and Flynn himself.
From his very first appearance in the pilot episode, "My First Day", the Janitor is evasive when asked about his past. However, by itting that it was actually him in The Fugitive, he gives Scrubs' biggest clue to his true identity. If the film exists within Scrubs' universe, then it's reasonable to assume that it exists as is - the show's pop culture references prove that movies and TV are generally unchanged - and so the transit cop would still be credited as "Neil Flynn". By referencing the actor's real past through the lens of the character, Scrubs connects the character to the actor who plays him, and with a character as mysterious as the Janitor, this perhaps serves as a clue to his true identity.
The Janitor's "Revealed" Identity Was A Clone High Reference
In the final episode of Scrubs season 8, "My Finale", the Janitor's real name is revealed. After eight years of being tormented by the custodian, J.D. finally asks him what his name is, only to be told the simple (and anti-climatic): Glenn Matthews. However, immediately after, another character is then heard calling him "Tommy", casting a little doubt over its authenticity. However, in line with this theory, there's perhaps another reason for the Janitor having chosen the name of Glenn Matthews.
The name of Glenn Matthews is actually confirmed to be a reference to Flynn's character in one of Scrubs creator Bill Lawrence's other shows, Clone High. Flynn voices Glen the Janitor in Clone High, leading to the theory that the Scrubs character may be the same person, but it's also possible that the name is a reference within Scrubs' universe, too. If Scrubs' Janitor is in fact really Neil Flynn, then he'd also have offered his voice to the character, so in a sense, Flynn is Glenn - meaning that it's technically not another of the Janitor's lies.
Scrubs Scripted Everyone But The Janitor
One of the most well-known and brilliant pieces of behind-the-scenes Scrubs trivia is that scripts were reported to contain the words "whatever Neil says" in place of the Janitor's dialogue. This is a testament to the comedic ability of Neil Flynn, but it also speaks to how much of his own personality he was able to inject into the character. Moreover, it potentially serves as an added piece of evidence for this theory.
Throughout Scrubs, the Janitor was rarely depicted as sharing any real common ground with any of the show's characters. The idea that his character is Neil Flynn even within the show's narrative is lent an added weight by the show's scripts, as every other character had their lines provided for them. By allowing Flynn to act as his natural self, Scrubs utilized his comedic talents, but the idea that his lines weren't scripted just further blurs the line between fact and fiction when it comes to the Janitor.
What The Janitor Being Neil Flynn Really Means
Of course, the idea that the Janitor is really Neil Flynn himself is something of a stretch, but the character's bizarre nature is very much in line with the theory. The character's connection to J.D. was written into the show as the reason that the Janitor didn't return for Scrubs season 9, but the real reason was that Flynn landed a leading role on The Middle. Flynn being unavailable to return led to the character's departure from Sacred Heart, and within Scrubs' story, he's shown simply walking out of the hospital, never to be seen again.
The Janitor really being Neil Flynn himself potentially reframes the show with the character at its core, which isn't entirely implausible given the Janitor's massive popularity. Scrubs always had fun with the character's fluid backstory that never truly established who the character really was, but the few clues the show did give all potentially prove this theory. Flynn's departure also contributed to the failure of Scrubs season 9, as he was such an integral part of the show's dynamic that it didn't recover without him. It's a theory that's as mind-bending as it is implausible, but it's still possible that Scrubs' Janitor was really Neil Flynn all along.