Here's why the Janitor didn't return for Scrubs season. Scrubs debuted in 2001 and followed the misadventures of medical intern J.D. (Zach Braff), with the first episode detailing his hectic first day at Sacred Heart Hospital. While J.D. has constant, bizarre daydreams and wacky narration, the show wasn't shy about showing the stresses and drama of working in a hospital. Outside of the Janitor (Neil Flynn), other major characters include fellow intern Elliott (Sarah Chalke), J.D.'s best friend Turk (Donald Faison) and his gruff Scrubs' mentor Dr. Cox (John C. McGinley).
Scrubs was a unique blend of comedy and medical drama that proved a hit with viewers and ultimately ran for nine seasons. This wasn't the original plan, as season 8 was supposed to be the end of the series. Its finale episode "My Finale" closed with an emotional, heartfelt sequence of J.D. working out of the hospital for the last time as he imagines most of the key characters from the series saying goodbye.
J.D. also learned the real name of his Scrubs nemesis the Janitor during "My Finale," which was Glenn Matthews. J.D. first earned the Janitor's wrath during the pilot, where he casually suggests a door the Janitor is fixing won't open because it has a penny stuck in it. Scrubs' the Janitor reads this as a sign of guilt and sets about playing pranks on J.D. and generally making his life hell during his time at Sacred Heart. When Scrubs was renewed for season 9, it switched focus to new med students coming to the hospital, with Braff only returning for six episodes. Flynn also reprised the Janitor for one brief scene, where he quits upon learning J.D. has left the hospital for good.
Turk recounts this to J.D. in the first episode of Scrubs season 9, who explains the day after J.D. left and the Janitor realized he wasn't coming back, he left on the spot and was never seen again. The Janitor not returning for Scrubs season 9 is really a consequence of Flynn landing a lead role in sitcom The Middle, which itself ran for nine seasons. While Flynn's presence was greatly missed, since Scrubs season 9 is commonly considered the show's worst, it worked out in the actor's favor ultimately.
If anything, his abrupt exit from Scrubs was the perfect way for the Janitor to leave. Much of his past was left mysterious throughout Scrubs, though it's known he worked as an actor, even appearing in Harrison Ford's The Fugitive - which was really footage of Flynn's own small role in the 1993 blockbuster - so it's good he disappeared with little explanation. That said, if a Scrubs reboot ever happened, he'd almost certainly return to torment J.D. once more.