Despite JD being Scrubs' narrator, Doctor Cox could actually be the show's real main character. Scrubs follows the career of John "JD" Dorian as he progresses from an intern at Sacred Heart hospital to one of its resident doctors, before moving away in what some fans consider JD's perfect Scrubs ending. JD's journey is seemingly central to Scrubs' narrative, particularly as he narrates the show, and each episode is filled with his zany imaginings in the guise of cutaway gags.
Along the way, JD meets a number of colorful characters who help him on his journey and shape the man he becomes. Not the least of these is Dr. Percival Cox (John C. McGinley), who acts as JD's often unwilling mentor and occasional bully. Cox's journey over the course of the show is as filled with character development as JD's, making him as vital a part of Scrubs' narrative as any of its prominent characters.
The pair's stories are so intertwined that one fan theory believes Cox and JD are the same person, which goes some way toward proving Cox's importance. However, upon re-examination, it's entirely possible that Cox is actually Scrubs' main character, not least because his journey is such a central part of the show. Later seasons actually focus as much—if not more—on Cox as they do JD, exploring his roles as a mentor, doctor, father, and partner simultaneously, lending the theory even more weight.
Cox was always one of Scrubs' best characters, delivering most of the show's memorable moments - be they dramatic or comedic - and without him, JD's character development likely wouldn't have happened. Scrubs sees JD become a confident and capable doctor under the watchful eye of Cox, and as early as Scrubs' perfect pilot, "My First Day", he's the guiding force behind the show's story. Cox is arguably more crucial to Scrubs' narrative than JD is, as he's the character that all others look to in order to resolve their problems.
There's also the matter of Scrubs' ill-fated season 9, which saw the introduction of a new cast and a tweaked premise shifting the focus to medical students. In season 9, JD's role is reduced to that of a recurring character, whereas Cox's role remains the same: the gruff, hard-to-please mentor. Having Cox continue on in the same role when so many other characters did not actually makes him the most consistent part of Scrubs. While Scrubs season 9 was a near-perfect spin-off, it was widely despised by fans for its shifting of focus, but seeing Cox as the show's main character actually fixes this problem somewhat.
Cox may not be the show's narrator, but he's central to its overall story and most of its other characters' development. Viewing Scrubs through the lens of Cox as its main character makes the show less about JD's career progression, and more about Cox's: he starts as a doctor, then through his mentoring of others becomes a teacher, softening in the process. Whether or not Cox could ever truly be considered the main character of Scrubs, the theory reframes the show's story in an interesting way.