J.D. tries to persuade a smoker patient to quit smoking in order to impress Dr. Cox, who is just feeling lonely in his opinion. Elliot's attitude towards Carla annoys her, thus Turk is able to go on a date with Carla, when he convinces her to forgive Elliot.

J.D. has finally earned the spot as brightest student, but he's got competition: Nick Murdoch, who seems to be nicer, friendlier and has a better butt than him. But even J.D. can't hate the guy, for he is so nice. But he is surprised when he finds Nick sitting in a corner crying because he can't take the pressure of medical internship. Meanwhile, Turk is having problems at the operation table and doesn't tell Carla, who keeps bothering Dr. Cox about it. And Dr. Cox gives Turk a very unique suggestion on how to calm down before surgery.

A woman slips and falls on the wet floor of the hospital. Afraid that she might sue the hospital, Dr. Kelso asks J.D. to stand by her and be friendly, so she won't sue them. But J.D. is very busy with Dr. Cox's 24-hour marathon to keep his ICU patients alive.

Elliot is desperate for some attention from Dr. Cox. Meanwhile, Turk snaps at Carla when she steals fries from his plate.

J.D. is frustrated when his budding romance with an ex-patient wilts as their dates are constantly interrupted by emergency calls, while the beastly Dr. Kelso becomes less fearsome to the wide-eyed interns, when Dr. Cox informs them how to avoid the blowhard's bite. In addition, a perplexed Carla and Turk deal with their first sexual intimacy complication.

Turk's competitiveness is starting to annoy J.D., especially when it crosses the line of personal jokes and comes to patient's matters.

Meanwhile, Dr. Cox finally has a taste of good coffee, but thanks to his feud with Dr. Kelso, the only nurse who was able to make it gets fired. Elliot meets a very attractive patient, whom she instantly identifies, but has a really hard time getting him to ask her out.

Jordan's brother Ben is admitted at Sacred Heart for having an accident with a nail gun. J.D. learns that Ben has leukemia, but won't believe it, since there have been many mixups in the hospital lately, so he goes on a search for the real test results.

Ben takes the news of his diagnosis pretty well - at least better than his sister Jordan and J.D. Remarkably, it is Dr. Cox who is the voice of reason and compassion, until his own fears get in the way.

Meanwhile, Turk and Elliot have their own issues to deal with. Turk is upset because he wasn't chosen to assist on a difficult surgery and Elliot is criticized during rounds by Dr. Kelso for the 100th time.

When Dr. Kelso challenges the residents by offering a trip to a medical conference in Reno as a reward to the individual, who presents the most interesting case study, J.D. refuses to play along, earning him the respect of Dr. Cox.

In the meantime, Turk misses his opportunity to ask for a new laser on the one day of the year, that Dr. Kelso grants favors, so he is forced to find another way to come up with the goods.

J.D.'s brother is in town. Turk is thrown out of a patient's funeral for not knowing his name and feels even worse because earlier he made a bet with Dr. Cox over another patient's life.

Elliot meets a nice guy at the bar, but freaks out when she finds out he's a male nurse at Sacred Heart. Turk keeps asking Carla to marry him, but she still won't give an answer. Dr. Cox feels the pressure he puts on himself everyday: His psychiatrist, his subordination to Dr. Kelso and his paternal feelings for J.D.

Turk takes J.D. up to surgery, and right from the start J.D. steps all over Turk when trying not to be the geek among the surgeons. Paul hears Elliot say "I love U2" while she was rearranging her CDs and thinks she said "I love you too." Dr. Cox decides to get even with Dr. Kelso by telling everyone he's dead, revealing what people really think of him.

J.D. carries on with his romance with Jamie, but finds himself at a dead end after realizing she's a drama queen. Dr. Kelso makes Dr. Cox give a class on how to approach the patients nicely in order to prevent possible law suits. Carla's mother dies and she wants to get married.

J.D. and Turk's college buddy, Spence, drops by for a visit, and accidentally tells Dr. Cox a secret. Too much partying with successful Spence causes Turk and J.D. to show up late and drunk for work, which Dr. Kelso fully reprehends them for. Elliot's feeling low since she can't measure up to Dr. Kelso's standards, and the Janitor starts another feud – this time over paychecks – with J.D.

Finding difficulties training his interns, J.D. asks to Elliot for some help. She tells J.D. about Sean, who gave Elliot great tips based on his dolphin training that fit perfectly for her interns.

Dr. Cox finds the ideal pediatrician for his son: Dr. Norris, who acts and looks just like him. However, Dr. Cox is quick to find a problem with him once Jack develops a cough that scares both him and Jordan.

A chance meeting in the elevator sparks a new friendship between J.D. and the mysterious Danni whose ongoing dialogue about her ex forces J.D. to talk about his feelings for Elliot.

Carla's brother Marco comes to visit, but he still hasn't forgiven Turk for mistaking him for a valet at their mother's funeral. Unfortunately, Turk can't even apologize because Marco can't speak anything but Spanish.

At the hospital, Dr. Cox relishes his new job promotion but is surprised when J.D. doesn't follow his lead in contradicting Dr. Kelso's orders.

Elliot struggles to find her defining moment after Turk performs his first solo surgery. Dr. Cox deals with the reality of growing older when his back goes out. J.D. finds out that many of the hospital staff don't know the Janitor as he does.

Elliot feels uneasy with the proper terms for sexual organs, especially after performing a pelvic exam; J.D.'s patient refuses to have surgery for prostate cancer.

J.D. tries to break-up with Danni, but she beats him to it when she realizes that she will always be second place to Elliot in his heart.

Dr. Cox suddenly becomes a nice guy and Elliot changes back to her old self after Dr. Kelso criticizes her new look.

J.D. believes he may have finally found a mentor in Dr. Kevin Casey, a surgeon with obsessive-compulsive disorder, and it turns out that Dr. Cox has always been jealous of the guy.

Meanwhile, the Janitor and his new assistant help Kelso out with a garbage problem.

Elliot finds herself perplexed over a simple procedure that leaves her questioning her career path. She goes to seek Dr. Kevin Casey's advice but becomes frustrated when she learns that the epiphany toilet, which the Janitor secretly installed on the roof, is getting more attention than she is.

Meanwhile, Turk asks J.D. to be his best man at his wedding, which sends J.D. into sheer bliss momentarily until he hears a phone message that makes him question his friendship with Turk.

The big day for Turk and Carla has finally arrived, but a patient holds up Turk.

With Elliot still angry at him, J.D. attempts to reconcile her with Sean as a way to make everything right again in their friendship.

Dr. Clock tries to reconcile J.D. and Eliot, while waiting to see which one Dr. Cox will give the Chief Resident position to. Molly and Carla are experiencing some subtle conflict and Elliot and J.D. begin to come together after long bouts of conflict of their own.

Meanwhile, Dr. Cox, Turk and the Janitor are forced to work together to help a patient.

J.D. is shocked to hear Dr. Cox tell his interns that eventually, they will screw up and kill a patient. J.D. fears his first time killing someone will soon be upon him.

Elliot is upset with Molly, after she disagrees about a patient's promise to attend drug rehab.

Carla loses Rowdy and she and the Janitor go looking for him.

When Molly takes a job at a different city, she and J.D. end up having a night of kissing, and he tries to rush to sleep with her before she leaves.

Dr. Cox goes on ambulance duty with a maniac, who he eventually finds out is a woman who has lost her son to an accident.

J.D. is approached by a malpractice attorney, asking him to do a risky procedure on her father.

Meanwhile, Elliot guides Doug to a new career path and Turk struggles to avoid a hypochondriac patient.

Elliot starts showing J.D. up as the calmer, more competent doctor. A date with the Janitor leads to an a capella sing-off between his "group" and Ted's band.

Turk starts taking his diabetes more serious, when he realizes the dire consequences of the disease.

J.D. tries to impress Kylie by paying a hobo in the hospital to fake a heart attack, when everything becomes boring due to a quarantine that he caused.

Turk learns, that Carla dated Cox and gets mad at her for not telling him.

The Janitor makes a bet with Dr. Kelso, who is starving, that will make him pay $700, unless the Janitor is able to get a "face cake," in order to satisfy him, from Laverne.

Also, Danni Sullivan returns to annoy everyone, causing a constant fight between Ted and Doug.

J.D. ditches a seemingly uninterested Kylie for Dr. Molly Clock, who just returned from Milwaukee.

Carla fumes over Turk's frequent phone calls to an ex-girlfriend.

The Janitor and Dr. Cox make a wager over Elliot.

Elliot is torn between moving too quickly and ruining her new relationship with Jake.

Dr. Cox teaches Turk about having a healthy ego and Dr. Kelso and the Janitor fight over who gets to use the motorized cart.

While planning his birthday, J.D. finds a list of things he wanted to accomplish, before he turned 30. He enters a triathlon to begin. Meanwhile, Elliot discovers a side of her boyfriend Jake, that freaks her out. And Turk is working hard to impress his bosses and takes on a patient, who wants to be hypnotized during surgery in effort to be promoted.

Dr. Cox's religious sister Paige comes to visit for her nephew's baptism. Turk is finding out, just how unsexy baby making can be. Elliot helps him realize that Carla finds the whole process to be romantic. Elswhere, J.D. and the Janitor start a buddy friendship.

In a "Wizard of Oz" homage, J.D. is trying to go home, Turk searches for a heart donor and Carla worries, that she doesn't have the courage to become a parent. Meanwhile, Elliot doesn't believe, that she has the brains to lead a question and answer session. Also, the Janitor is painting color coded lines throughout the hospital for easier navigation.

J.D., Turk, Elliot and Carla are interrogated about the mysterious death of a patient.

Dr. Kelso learns, that J.D. and Turk were away tracking down a patient, Elliot was traumatized over finding out that her make-out buddy was married and Carla was busy recruiting hospital personnel for a group lottery purchase.

J.D. is still dealing with his recent breakup and trying not to kill intern Keith, who has become annoyingly perfect. To make matters worse, a favorite patient is in a serious coma and each of the staff finds their own way to deal with it.

Dr. Cox and the Janitor bond over drinks at the bar and Carla makes it her mission to make the hospital's gym female friendly. Meanwhile Turk suggests, that J.D. and Elliot find themselves 'booty calls'.

J.D. urges Cox and his fellow doctors to do special, unconventional things for their patients, but J.D. himself is not sure he can shave his head for a woman undergoing chemotherapy, after meeting a woman who loves his hair. Meanwhile,Turk and Carla attempt to eliminate all the stress in their lives, to better their chances of conceiving. Also, Elliot can't stop giving her new boyfriend Keith stupid gifts.

J.D.'s brother Dan returns for a surprise visit and Elliot learns that J.D. has been telling Dan that she still likes him. A patient with weight-related problems needs an MRI, but he's too big for the machine. Carla and Turk freak out when they begin to discuss baby names. Meanwhile, Dr. Kelso assigns Dr. Cox to assist Ted with malpractice claim paperwork after Dr. Cox insults Dr. Kelso's son.

J.D. plans a date with Kim on their night off but Elliot keeps getting in their way. Meanwhile, Elliot throws a baby shower for Carla.Perry and Jordan hand over all of Jack's stuff to Carla. And someone announces a very surprising pregnancy.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.