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J.D. says his final goodbyes during his last day at Sacred Heart in the Scrubs Series Finale.
J.D. decides to move closer to Kim to be near his son and gets a job at the local hospital there, St. Vincent's.
In an effort to move closer to his son, Sam, J.D. reaches out to Kim (Elizabeth Banks) only to find out she's dating Elliot's ex, Sean (Scott Foley). Meanwhile, Turk rallies to the troops at Sacred Heart to get him promoted to chief of surgery.
With everyone in the Bahamas, the Janitor and Lady get to have their ceremony in part two.
The Janitor and Lady send out fake invitations for a wedding in the Bahamas to get presents, but everyone from the hospital accepts.
Turk and Elliot attempt to scare the interns by telling them it's a Full Moon out and the worst patients come out.
The interns give the Sacred Heart senior staff some insight. J.D.'s ego goes nuts when Cox gives him a momentary nod.
Turk tries an experimental procedure; Dr. Cox puts on his old ring; Janitor has problems with Lady
J.D. and Turk put on a skit show where the interns make fun of the senior members of the staff. Denise and Sunny have to deal with a patient with an overprotective mother.
Elliot attempts to deal with J.D. being gone and Carla tells Turk they're having a second child.
Ted finally meets a lady in the form of Stephanie, a ukulele player at the hospital. Cox has to find time to be Chief and not give up the things he loves.
Dr. Cox slowly becomes better friends with Dr. Kelso as he tries to adjust to being Chief of Medicine.
Dr. Cox is offered the Chief of Medicine position and J.D. and Elliot try to rekindle their sexual romance.
J.D. tries to teach his intern, Denise, to feel compassion towards her patients while Elliot tries to get Turk to use her intern to help in his research paper.
J.D. and Elliot reignite their past feelings when they team up to try and get Dr. Kelso to branch out beyond the Coffee Bucks.
Dr. Kelso and Cox team up to oust Dr. Maddox from Sacred Heart. Carla takes on a self-centered, incompetent intern.
This episode focused on a patient George Valentine (Glynn Turman) who had just one night to live and no family to spend it with. J.D. and Turk give up steak night to spend it with him.
Dr. Maddox (Courteney Cox) comes in as a replacement for Dr. Kelso. Meanwhile, J.D. struggles to manage the new interns and Carla puts Elliot's ego in check.