Jordan's brother and sister return, but Dr. Cox learns that his brother-in-law Ben hasn't visited a doctor about his cancer in the two years he has been gone traveling the world.

J.D. asks Dr. Cox out for lunch, but runs into annoying former patient Jill Tracy, who unexpectedly teaches him something about responsibility. Elliot and Carla discover that Todd has been lying about all his hospital "conquests" and suspect that he's been less than truthful about other issues. Turk warns them not to meddle in his affairs.

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.

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.

Dr. Cox starts drinking after his decisions result in the death of three of his patients. The staff tries to cover for him at the hospital, while everyone tries to convince him how inspiring he is for them. Turk starts his new rotation with orthopedic surgery, but isn't so fond of his attending doctor's touchy-feely methods. Thus, J.D. and the Janitor attempt to help Turk find ways to bond with his new supervisor.

The three interns are each assigned patients with various illnesses. Statistically speaking, one of the three is going to die. J.D.'s patient is 86 year old Mrs. Tanner, who is in renal failure. 20 year old David Morrison is Turk's hernia patient and Elliot's patient Mrs. Guerrero only speaks Spanish and might have lupus.

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.

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.

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.

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.

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.

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.

When Dan resurfaces, J.D. is shocked to learn his father has passed away. The reactions from his co-workers help J.D. a little, but the one person, Dr. Cox, who he wanted to be there for him is too busy with J.D.'s patients. Meanwhile, Dan sits drunk in the bath tub the whole day and Turk finds out he has Type II Diabetes.

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.

It's J.D.'s last day as an intern, and soon he will become a resident. Carla and Turk are arguing about dating other people. Elliot finally rebels against being everyone's doormat, and J.D. is just trying to stay out of people's way. Jordan has returned to get a physical and a new patient, Mr. Bober, has been admitted, because he needs his gall bladder removed. He really needs the surgery, but doesn't have the insurance to pay for it. They enlist the help of Dr. Cox, Dr. Wen and Jordan.

As J.D.'s relationship with Danni progresses, he and Dr. Cox are forced to spend more time together outside of the hospital, to Perry's great chagrin. Meanwhile, as they each deal with problems in their own relationships, Carla and Elliot work to find their own balance between their personal and professional relationships. Dr. Kelso accidentally punctures his eardrums giving the hospital staff an opportunity to tell him how they truly feel about him.

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.

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.

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.

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.

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.

An ever present butterfly prompts the question on what could have happened different as Turk looks for his lucky do-rag for surgery, and Elliot tries to find a lost stuffed animal for a child needing a bone marrow transplant.

Elliot asks Sean to move in with her, which only adds to J.D.'s problems. Turk is unsure why Dr. Miller's attitude towards him has changed, until he finds out that Carla un-invited her from their wedding. Dr. Kelso outrages Dr. Cox when he announces that Sacred Heart will begin doing full body scans, starting with an ever present hypochondriac patient, who wants any freebies he can get.

When J.D. has to address a bunch of pre-med students about what it's like to be a doctor, he strays off the beaten path and chooses to discuss his best moments as a doctor instead. When he challenges the rest of the staff to do so, they all remember their best memories in the medical field. Meanwhile, Elliot is forced to face her fear of children, when she must befriend a ten year old boy, whose father is being treated in the I.C.U.

J.D. meets the klutzy Julie, and when he becomes smitten, Elliot attempts to help out with romance advice. Meanwhile, Carla tries to find Dr. Cox's soft side, when he refuses to kiss his son. Turk and the Janitor put together an air band to win a contest, but Kelso gives them a tremendous obstacle.