Scrubs focuses on the lives of several people working at Sacred Heart, a teaching hospital. It features fast-paced dialogue, slapstick, and surreal vignettes presented mostly as the daydreams of the central character, Dr. John Michael "J.D." Dorian.
Turk and Carla turn J.D.'s old bedroom into a nursery for the baby. The Janitor seizes an opportunity to shove J.D. out of the picture for a day. Elsewhere, Elliot uses her mother to learn information about Keith's peers and Turk & Dr. Cox accuse each other of not being hip.
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.
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. 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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
In the aftermath of their near-indiscretion, Elliot realizes she doesn't want to be with Keith, and J.D. resolves to stop sabotaging himself. Meanwhile, Dr. Cox and Turk find a patient they both like who is in danger of being discharged.
Kim goes into labor, and J.D. struggles to decide if he should tell her what he really thinks of their relationship. Turk, desperate to do something not baby-related, races to beat a video game before Carla discovers him. And Dr. Cox searches for someone he trusts enough to give his daughter a shot.
J.D's brother Dan returns and delivers a few home truths to his little brother. In the meantime, Elliot and Dr. Cox debate over the morals of their practice and the staff of Sacred Heart find the Janitor's behavior rather odd after he watches "An Inconvenient Truth".
Turk tries to assure a worried Carla that their daughter will acknowledge her Latin heritage. Meanwhile the Janitor challenges J.D. to identify everyone in the hospital, when it is discovered that he uses nicknames, because he doesn't know the people's actual names. If J.D. can't name all of them, he must take up the mop for a day. Elsewhere, Dr. Cox realizes that he is lonely without his wife and children.
The Sacred Heart staff has to deal with their inner child, when J.D. and Turk remember their first prank, Dr. Cox has a ten year old Leukemia patient and Dr. Kelso celebrates his birthday.
Though Elliot boasts that through private practice she gets to get to know her patients, nobody seems to care. Carla is amazed at how the Janitor was able to score such an attractive girlfriend. The doctors are improving their services to get a higher ranking on a website and although J.D. appears nonchalant initially, he is elated when he is ranked #1.
J.D.'s teenage burn patient gives him a hard decision to make when he wants to go to his high school graduation. Turk doesn't want Carla to find out that he secretly learned Spanish. And to address Dr. Kelso's weight gain, Dr. Cox makes a game out of stealing his breakfast.
When Dr. Kelso tells the Janitor that nobody cares what he thinks, he starts a newspaper called "The Janitorial" to prove him wrong. J.D. and Turk fight over their manhood issues, while Dr. Kelso is too proud to ask for help about one of his problems.
Dr. Cox had a patient that he hadn't been able to diagnose for two years, and he is back again. Dr. Kelso has to face a retirement board when his true age is revealed. Elliot and Carla try to find enough people in favor of Dr. Kelso to keep him as Chief of Medicine.
Elliot and J.D. discover a major change in their relationship, when they spend time together looking for a former patient. Dr. Cox contemplates his new job title, when Ted refuses to do the majority of his work, whilst Carla and Turk talk about the possibility of a second baby. Meanwhile, the Janitor claims Dr. Kelso's abandoned office for the brain trust.
After a hard day of work, Dr. Cox has the burden to tell his son Jack a good night story, so he disguises his hard day as a fairy tale about the little village Sacred Heartlia with Carla and Turk as the two-headed witch Turla, Elliot as the princess and J.D. as the village idiot. Other people featuring are the Janitor as the giant, Keith as the prince, Dr. Kelso as the dark lord Oslek, Ted as his hunchback and of course Dr. Cox as the brave knight.
J.D., Turk, Cox, Kelso and intern Denise return to Sacred Heart to teach med school, while new med students Lucy, Drew, Cole and Maya are put through the wringer on their first day of school.
Lucy learns a hard earned lesson about what it takes to be a doctor. Meanwhile J.D. and Turk spot a potential love connection between Denise and the new med student, Drew, as they play matchmakers with a little bit of help from Dr. Kelso.
J.D. and Drew learn a tough lesson in mentoring when Dr. Cox and Lucy show them that sometimes the student is the teacher.
While their wives are out of town, J.D. and Turk attend a med student's party; Kelso says goodbye to Ted and Gooch.
J.D. still clamors for Dr. Turk's approval as he approaches his final day of teaching at Sacred Heart, Lucy searches within herself for the courage to perform a basic medical procedure on a real human, and Denise and Drew make things official.
While Turk struggles to find a replacement best friend, Elliott offers some sound advice and guidance to an over-worked and exhausted Lucy.
Before receiving their white coats, the med students of Winston University must figure out why they want to be doctors, and Denise gets a little relationship help from Elliot.
Lucy finds couplings, dysfunctional or not, throughout the hospital
When Cole and Kelso both get negative results back after a few routine tests, they learn the hard way to put their egos in check in order to rein in the support of their so-called friends.
The med students of Winston University finally find something to be thankful for when Cole identifies his true calling in surgery, Drew finds the love of his life, and Lucy finds the inspiration to become a doctor.
Dr. Kelso's beautiful but unethical replacement, Dr. Maddox, shakes things up at Sacred Heart, while J.D. struggles to manage a new crop of incompetent interns and Carla helps Elliott put her ego in check.
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.
Dr. Kelso and Dr. Cox have to work together again to get rid of Dr. Maddox, while Carla faces an incompetent intern.
J.D. and Elliot's relationship seems to have been rekindled when they encourage Dr. Kelso to find his true happy place.
Featuring a special appearance from Sesame Workshop's "Muppets", J.D. learns a lesson about the gift of compassion, while Elliot gets scammed by intern Katie to secure a spot on Turk's team.
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.
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.
It's Ted's lucky day when he falls head over heels in love with an ukulele player, and Dr. Cox realizes he cannot handle everything that is thrown at him.
J.D. manages to still bother Dr. Cox despite being away on a vacation from the hospital. Meanwhile, Turk and Carla have some big news to announce.
J.D. and Turk gather up a new crop of interns as they organize their annual (and historically unfunny) sketch show.
While Turk views an inspiring story on SportsCenter, he comes up with a new procedure which may help a paralyzed teen. Meanwhile, Dr. Cox and the janitor are suffering from romantic problems
J.D.'s ego becomes inflated after Dr. Cox finally gives him the recognition he's been waiting for. Elsewhere, the senior staff receives insight from the interns.
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.
The Janitor and Lady invite the Sacred Heart staff to their fake wedding in the Bahamas hoping to score some loot but their scheme is about to backfire...
The tropical seaside wedding goes ahead as the Janitor and Lady tie the knot which affirms the relationship of another couple.
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.
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.
J.D. is planning on leaving Sacred Heart but before he goes there are a few things that he wants to do including; getting a hug from Dr. Cox, and learning the Janitor's real name. Elliot is ready for the next step in her and J.D.'s relationship and she begins moving her furniture into J.D.'s apartment.