In the season finale, J.D. and Elliot start thinking about their future and if they both made a mistake in not being with each other. The Janitor activates the "Brain Trust" to come up with the perfect wedding gift for Elliot.
Kim moves in with J.D. in order to raise their child together. J.D. learns from Turk and Dr. Cox that fatherhood changes the way of how to see things. Carla complains to Elliot about her being a control freak when they prepare the bachelorette party.
J.D. and Turk go to a medical convention in Phoenix, Arizona, where they run into J.D.'s ex-girlfriend Dr. Kim Briggs, who has a surprise for J.D. Meanwhile at Sacred Heart, the janitor pretends to be the chief of medicine and Dr. Cox starts to put doubts about the wedding into Elliot's mind.
J.D. tries to get together with Elliot's sorority sister Melody, but she just wants to make out with him without going further. Meanwhile, Keith re-proposes to Elliot after she gets to make everything perfect, while everyone has fantasies about being married to Elliot. Elliot and Carla are having problems figuring out what is wrong with two elderly patients, who show the same symptoms but have no obvious connection.
When Keith leaves town for a few days, J.D. expects that he'll finally be able to spend some quality time with Elliot. But he doesn't anticipate Elliot's old college friend dropping by. J.D. switches between hitting on her and competing with her for Elliot's attention. Meanwhile, Turk and Dr. Cox volley a hypochondriac patient back and forth since there's nothing wrong with him.
The perspective shifts between Jordan, Ted, and Todd, as they go about their day. Jordan messes with Elliot and Keith's relationship and is disturbed when it doesn't give her any satisfaction. Ted tries to settle a pay dispute between the nurses and Dr. Kelso. Todd has found his calling in plastic surgery, but must convince Turk not to interfere with a sixteen-year-old girl getting breast implants.
In the wake of Laverne's funeral, the Sacred Heart Staff decide to implement lessons from her life to their actions. Carla is upset that everyone seems to act as if nothing has changed. Dr. Cox tries to take twenty minutes for himself every day, but has great difficulty doing that. Meanwhile, the Janitor helps J.D. and Turk treat a deaf patient. And Elliot learns that Keith wants more from their relationship.
Laverne is brain-dead, and her family decides to take her off life support. One by one, the staff say their goodbyes, except Carla, who stoutly refuses to accept what's happening. She consequently finds herself "haunted" by Laverne. Meanwhile, Jordan gives birth, but Dr. Cox doesn't want to tell anyone because he doesn't want his daughter's birthday to always be associated with Laverne's death.
Laverne and Dr. Cox engage in a philosophical debate. Carla finds a hot nanny for Isabella, and Turk struggles to find a way not to leer at her. Elliot smuggles a patient's dog into the hospital to cheer her up and ends up in hot water with Dr. Kelso. A tragic twist awaits at the end, challenging everyone to decide if they think everything happens for a reason.
J.D. and Turk try to treat Dr. Kelso's uninsured friend. Meanwhile, Dr. Kelso himself is concerned about a clothing thief. Elsewhere, Dr. Cox tries to convince Elliot that a reformed drug addict isn't exactly clean, and the Janitor blackmails Carla.
When Private Dancer is released from the hospital, the military informs him that his injuries are too severe to be reinstated into the service, so he gets depressed. The Sacred Heart staff try to cheer him up, while the Janitor is having a fish problem.
A memory loss patient is the peg for a look back on the last seasons of Scrubs, when the Sacred Heart crew looks back at their memorable moments.
J.D. develops a crush on a new physical therapist but due to his latest misfortunes, he finds it difficult to ask her out. Elliot asks Keith to move in with her, but is not willing to budge on her home rules. Turk breaks his arm and is sent back to residency by Dr. Kelso. Thanks to Dr. Cox, he realizes that he doesn't know as much about medicine as he thought.
A Croatian Doctor comes to Sacred Heart, only to find out that he has to redo his Internship there. J.D. shows symptoms of 'Vasovagal Syncope', a condition that causes fainting and blackouts. Turk and Elliot argue over whose turn it is to take care of him, whilst Carla tries out her new excuse "I have a baby" and the Janitor takes a vacation.
After being convinced to go to Tacoma for Kim's first ultrasound, J.D., along with Carla, Elliot, Janitor, Keith and Ted, takes Kelso's new RV on a road trip. Meanwhile, Jordan and Dr. Cox have trouble when Jordan's ultrasound reveals that the baby will need surgery.
The hospital is seen through the eyes of Dr. Kelso, who befriends an Iraq War veteran. The soldier's stay sparks a political debate among staff members.
A new patient at the hospital wakes up and sees everything happening around her as a musical. Carla can't decide whether or not to return to work and Elliot must find a way to tell J.D. he can't move into her new house with her.
Elliot begins enjoying luxuries since she has extra money with her new private practice gig. But eventually, J.D. becomes jealous of her and that forbids him the use of these privileges. Dr. Cox and the Janitor become roommates in one of the hospital suites, while Turk tries to convince Carla that she has postpartum depression and that she needs help.
Dr. Cox feels like the TV character House when he has to solve several mysteries, one of them being Elliot's anger towards Dr. Kelso, while for some reason she is taking it out on Turk. J.D. tries to be a better boyfriend to Kim.
J.D. and Kim are surprised of how much they have in common. Recently giving birth, Carla doesn't want to return to work. Meanwhile, Elliot tries to persuade Dr. Turner, a surgeon with thirty years of experience, that medicine is the better option to work with and that surgery could kill him.
J.D. and Kim start contemplating about their future and their baby's future. Meanwhile, Turk rushes Carla to the hospital after she goes into labor. And Jordan accuses Dr. Cox of not being a more defensive father towards Jack.
J.D. addresses the news that he is going to be a father and Dr. Cox is worried about how his anger is going to impact his offspring. Meanwhile, Carla and Turk prepare for the impending arrival of their new baby. Elliot feels left out because she is childless, while the Janitor wonders if he has wasted his life.
