JD tries to do right by Elliot. Turk and Carla find a bump in their marriage when Carla starts to dictate how Turk should be. Elliot makes friends with the new psychiatrist Dr. Molly Clock. When Carla lets Turk off the leash to get a new car, he instead buys himself a Vespa.
JD and Elliot both vie for the position of chief resident. Carla is irked when people start to trun to Dr. Clock for advice. Cox and Turk are at odds with each other when Turk delivers good news to a patient before Cox had the chance to, but the two combine efforts with the Janitor to remove a light bulb from a patient's rectum.
A momentary lapse in confidence affects the bond between JD and Turk. JD has a hard time being labelled as the Co-Chief Resident when Elliot is referred to as the Chief Resident. Cox and Jordan learn that their divorce was never finalized and immediately leap at each other's throats. Cox and Clark go toe-to-toe over a plastic surgery patient.
JD feels paralyzed by the thought that his actions as a doctor haven't killed anyone... yet. Carla decides that it is time for JD and Turk's stuffed dog to go. Elliot seeks Molly's help to get a patient an organ transplant, but it backfires when Molly decides to tell the truth to a panel of doctors.
Elliot finds a mentor in Dr. Clock, but her image of her is affected by Clock's choice in men. Turk and Carla have problems with their sleeping arrangement when Turk keeps waking Carla from her slumber.
JD's brother visits with the bad news that their father has died. The Janitor does everything he can to make Kelso think he's losing his mind.
JD is taken back when he catches Elliot dating his brother. Turk decides to use his newfound diabetes to his advantage. Cox and Kelso challenge Molly's optimism about humanity.
When Molly tells the staff she's leaving for another job, JD sees his one opportunity to hook up with her before she's gone. Cox spends his hospital mandated community service hours with a weird ambulance driver.
One of Cox's patients has a daughter who is a malpractice attorney which sends the hospital into a tizzy and Elliot tries to hide Doug. Turk gets a new call phone number.
Korman takes Turk to court over surgery's effect on his tennis game. Turk asks JD to give up Neena, who is acting as Korman's lawyer.
JD searches for a man's son in order to find a donor kidney. Jordan and Carly help Elliot learn to use her feminine charms.
JD's speech to some pre-med students inspires him to inspire his fellow doctors to look back on their best moments. Elliot confronts her fear of children.
J.D. and Elliot finally settle into a friendly routine as friends and colleagues. But, things get heated again when Elliot is viewed as a more relaxed and dependable doctor, putting her in more of an instructor's role to J.
The hospital is visited by a dashing Irishman who has an influence on Turk and JD's lives. Elliott and Carla get into an argument over making and breaking plans with each other. Cox has a pregnancy scare and decides to get a vasectomy without consulting Jordan, which leads to him getting a reversal. The Janitor decides to "bust chops" of people around the hospital.
While out clubbing with Turk and Carla, JD meets an attractive bartender and agrees to her request for a hospital visit. She brings her boyfriend with her who tests positive for VD. The Janitor wants to spoil a basketball game over Cox, who wants to watch the game on tape delay when he gets home, after Cox ruins a movie for him.
JD's first date with Kylie ends in disaster when they wind up back at Sacred Heart and in a SARS lockdown with the rest of the staff and JD's ex-Danni. JD tries to impress Kylie with a series of lies, but begins to feel guilty. Turk learns that Cox and Carla once dated and has a hard time coming to terms with the information.
When JD treats a sitcom writer, he wonders what life would be like if a sitcom writer was in charge of his reality.
Turk and Carla try to rescue their romantic ties by tossing JD to the curb. Cox and an old high school friend vie for supremacy. Cox believes that his friend's son my have autism, but has a hard time confronting the issue. Turk and Carla learn that JD might not be their problem.
JD thinks about his feelings for the visiting Dr. Clock which are compounded by the fact that he still hasn't achieved a true intimacy with Kylie. Cox and the Janitor make a wager over whether the janitor can get Elliott to go out on a date with him. Carla learns that Turk is speaking to an ex-girlfriend.
JD and Elliot try to help Carla and Turk as their marriage hits the rocks. JD takes Turk out, making him question whether marriage should be so hard. Elliot helps Carla get in touch with her dead mother. After Kelso confronts Cox on his bedside manner, Cox tells Kelso that he should try tending to patients. Kelso learns that Cox's tough love is his way of breaking through the cynical outlook of patients towards doctors.
JD tries to help Carla learn to trust Turk again, but they end up getting drunk and kissing. Elliot has a hard time handling a patient who mishandled erectile dysfunction medicine. The Janitor starts taking pictures of Cox with his son to provide to Jordan after Cox's son falls off the jungle gym and needs stitches.
Turk tries to decide who is responsible for the kiss JD and Carla shared and will have to face his silent punishment. Cox seeks out Elliot's help in dealing with a teenage girl who has stopped taking her epilepsy medicine. The Janitor's new uniform leaves him with a less than commanding look.
Turk and Carla start couples therapy. Elliot turns to Cox for help in landing a cute hospital visitor, Jake. Jake helped his elderly neighbor Betty decide about how to spend her final days on JD's say so and finds himself being threatened with legal action by her lawyer brother.
Cox takes the credit when Turk saves a taco stand patron to prove the point that it's fun to give yourself accolades. Elliot turns to JD for help in not losing her new beau Jake by getting intimate too quickly. Kelso abuses the staff from a Rascal wheelchair.
The interns all finish their residencies and Elliott is lured away by another hospital's fellowship. Carla worries that Jake controls Elliott. Jordan takes a part-time job at the hospital which annoys Cox.