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It's J.D.'s last day at Sacred Heart and the episode starts off with him weasling his way into some morning sex with Elliot. We find out that Elliot has slowly been moving into J.D.'s apartment behind his back. J.D. then goes into work expecting a grand goodbye, and at least is greeted with one from Turk who set up a giant goodbye sign for him. Since Turk blew his goodbye at the beginning of the day, the two vow to show equal excitement and hug each other every time they see each other.
J.D. only two patients during this episode: one who's mother is dying from the degerative brain disease Huntington's Disease. J.D. has to inform him that there's a 50% chance the son has it as well and they can test for it. The guy ends up deciding he doesn't want to know since they can't treat it and would rather have his fate in his own hands. J.D. can't remember his other patient's name or disease so he fires him.
It's also Kelso's "last day" of hanging around Sacred Heart. Unlike J.D. he gets a huge goodbye from everyone as he heads off to be a traveling doc for Locum Tenens. Kelso actually gives J.D. a so long sport.
Jordan, in an effort to be nice "for her stupid kids" gives J.D. a kiss goodbye cause after all, they did it once.
The Janitor spends the episode trying to get J.D. to admit to putting the penny in the door and J.D. finally does, saying it was by accident and he didn't want to upset the Janitor. Of course, we also find out the Janitor's name is Glen Matthews. According to him, J.D. just never asked before. Then again, someone walks by and calls him Tommy a second later so who ever really knows with the Janitor.
Carla and J.D. have a heart-warming goodbye as well. Carla affectionately calls him Bambi and he thanks her for her help over the years. All she wants is for him to say Turk loves her more than him... he says it's about equal.
Elliot eventually admits to having actually subletted out her old place. They officially live together.
Of course, J.D. spent the episode attempting to get a goodbye from Cox, including by giving Cox a goodbye present of all his rants written down in a book. J.D. manages to trick Cox into saying something when he thinks he's not around by bribing Sunny to trick it out of him. J.D. hears what he's been waiting to hear... that Cox thinks he's an exception Doctor, human being, and a friend. J.D. goes and hugs him.
The episode ends with J.D. have a dream sequence as he exits the hospital saying goodbye to almost everyone that's ever been on the show. He then has a dream about his future where he sees himself marrying and having kids with Elliot, their kids growing up with Turk's kids, eventually their kids marrying each other, and being friends with Cox. We can only hope that all comes true. The series crestor, Bill Lawrence, then gives himself a final cameo pulling down the Goodbye J.D. sign and saying the last goodbye.