J.D. points out what seems to be a technical mistake to Dr. Kelso, but it was really an attempt of Dr. Cox to save a woman without insurance using a dead guy's insurance. Dr. Kelso and Dr. Cox show J.D. their different ways of looking at medicine. Meanwhile, the Janitor intimidates J.D., Elliot discovers the healing powers of her boobs and Turk gives Carla a pen he thought he took from the Lost and Found box.

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.

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.

Renewed sex with J.D. calms Elliot, who's facing personal and professional dilemmas: She's broke, and patients are bailing out on her.

Jamie's (T.C.W.) husband died, and J.D. struggles with the ethical issues involved in starting a relationship with her. Dr. Cox babysits his son, whom Jordan still hasn't chosen a name for, and is disturbed that he feels nothing for the baby. Turk is haunted by erotic dreams about Elliot, which gets him into hot water with Carla.

Sean is a bit surprised and disturbed to learn about Elliot and J.D.'s history together, but it turns out his anger is really a cover up for his upcoming six month long trip and he doesn't want Elliot to explode.

Dr. Cox. is forced to swallow his pride and actually ask for help when he decides to throw his hat in the ring for the Residency Director position at the hospital.

Carla picks up an extra shift as a surgical nurse, which allows her to spend the day working alongside with Turk, to his great annoyance.

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.

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.

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. challenges an urologist's assessment on a consult for a patient in need of a risky surgical procedure. He also starts to fall for her. Meanwhile, Elliot considers breaking up with Keith, but Carla is showing extreme hormonal changes due to her pregnancy and tries to interfere. The Janitor and Dr. Kelso are having a little tiff of their own about fear.

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.

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.

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.

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.