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During the final moments of his last day, J.D. begins to wonder about the future after he leaves Sacred Heart...if his relationship with Elliot will survive, or if he will remain close to his best friend Turk, and even if Dr. Cox will miss him when he is gone.
J.D. is planning on leaving Sacred Heart, but before he goes there are a few things that he wants to do including having a moment with Dr. Cox. Elliot is ready for the next step in her and J.D.'s relationship, and she begins secretly moving her furniture into J.D.'s apartment. Meanwhile, Dr. Kelso is thinking about going back to work.
Change doesn't come easy for the gang when J.D. considers moving closer to his son. Meanwhile, Turk gets comfortable as chief of surgery, while Ted and Gooch reach a new level in their relationship.
Things get weird for J.D. when he discovers the identity of Kim's new man, as he plans to reach out to her in order to move closer to Sam. Meanwhile, Turk starts a campaign for a promotion, and Dr. Kelso is struck by an intestinal virus.
The tropical seaside wedding goes ahead as the Janitor and Lady tie the knot, which makes the other couples think about their relationships as well.
The Janitor invites the Sacred Heart staff to his wedding with Lady in the Bahamas on a three days notice, hoping to score some loot, but the scheme is about to backfire, when everyone decides to actually go there...
A combination of a full moon and some bad luck causes Sacred Heart's new crop of interns to receive their toughest case load yet, while Elliot makes an important decision regarding her future as a doctor.
J.D.'s ego goes out of control when he becomes the guy everyone in the hospital goes to for help with Dr. Cox. Intern Derek tries his best not to get involved, while Turk keeps trying to get his opinion. Meanwhile, the Janitor doesn't think Sunny is strong enough to be tortured.
Unable to deliver the news that a patient will never be able to walk again, Turk decides to try an experimental procedure instead. However, J.D. is worried that he is only giving false hope. Meanwhile, the Janitor and Dr. Cox face relationship issues that cause Elliot to intervene.
The new interns have to perform in the Sacred Heart traditional comedy show, so J.D. and Turk offer them to write the sketches. Meanwhile, the Janitor watches Carla in a delicate situation, and Elliot and her interns Sunny and Denise argue about a patient.
When J.D. goes on a mini-vacation, his only connection to the hospital is Elliot's cellphone. Meanwhile, Turk wants to spread the news of a second baby, but he does not get the reactions he expects. Somewhere else, intern Sunny struggles to keep a one year coma patient alive, about whom Dr. Cox does not care too much.
It's Ted's lucky day when he falls head over heels in love with a ukulele player, and Dr. Cox realizes he cannot handle everything that is thrown at him.
As his increasing workload from being Chief of Medicine begins to take a toll, the unimaginable happens when Dr. Cox reaches out to Dr. Kelso for friendship. Meanwhile, Elliot and Carla work on the doctor-nurse-relationships at the hospital.
Elliot and J.D. encounter a road block in their newfound romantic relationship, and Dr. Cox considers taking the now vacant Chief of Medicine post.
J.D., Elliot and Dr. Cox choose an intern to be their protegee. J.D. chooses Denise, but doesn't know how to deal with her inability to show emotions. Also, he keeps daydreaming with the Muppets. Elliot chooses Katie and sees her as a reflection. Therefore, Elliot tries her best to help her. Dr. Cox chooses Ed and spends the entire day trying to figure out why he hates him so much.
J.D. and Elliot's relationship seems to have been rekindled when they encourage Dr. Kelso to find his true happy place. Meanwhile, Dr. Cox has issues with the surgical staff, and the Janitor comes back to the hospital.
Dr. Kelso and Dr. Cox have to work together again to get rid of Dr. Maddox, while Carla feels she has to take care of intern Katie.
J.D. and Turk make a huge sacrifice concerning a decade-long steak night tradition for a dying patient. Meanwhile, Dr. Maddox, the new Chief of Medicine, begins to show her true colors.
The new Chief of Medicine causes a stir at Sacred Heart, while J.D. struggles to maintain the new interns, and Elliot has issues with her ego.
