The second season of the American comedy-drama television series Scrubs premiered on NBC on September 26, 2002 and concluded on April 17, 2003 and consists of 22 episodes. For the second season Neil Flynn was made a series regular. Colin Hay guest starred for the first time. It is also the first time an episode gives the narration to another regular, in "His Story." The show used a longer opening credits sequence for episodes 1 and 2, moving through the ward rather than just two beds, including a shot of Flynn as The Janitor, showing the names of the series regulars and ending with the chest X-ray showing the heart on the left side of the chest. NBC wanted longer content in the episodes so the credits permanently returned to the shorter version in episode 3, without Flynn nor actors names and with the mirror image chest X-ray.
Relationships between the staff of Sacred Heart Hospital have been shaken since Jordan's revelations. Turk is sleeping on J.D.'s bed, after Carla kicked him out of his own. Elliot is having a hard time facing J.D. every day at work. J.D. desperately tries to get Dr. Cox's attention back, unsuccessfully.
J.D., Elliot and Turk find themselves alone in the hospital night shift and face responsibilities without supervision for the first time. Luckily, they have Carla there to support and guide them through the night. Meanwhile, Dr. Cox doesn't know what to do, when he realizes that he has feelings for his ex-wife Jordan and is asked (forced actually) to introduce Dr. Kelso at a social event, where he will be receiving an award from the medical board.
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. insists that Carla should open up to him. When she finally starts to do that, J.D. screws it up by telling Turk. Elliot is desperate for attention from Dr. Cox. Turk sees himself in an ethical dilemma when Dr. Kelso picks him over a female surgeon to spend a weekend in Mexico.
Elliot sleeps with a handsome doctor she hardly knew and soon becomes the hospital tramp. Turk suffers from his back after operating with Dr. Amato, a very short surgeon. J.D. finds out that wearing a white coat doesn't make him a better doctor, but is upset by having Dr. Cox throw in his face that he made another mistake. And Dr. Kelso is just dying for an opportunity to lash out his anger on Dr. Cox.
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.
All of the male doctors are euphoric due to the visit of Julie Keaton, the pharmaceutical sales rep, except for Dr. Cox, who still believes in treating patients for their best health, instead of trying to get some attention from the hot Ms. Keaton. Meanwhile, J.D. and Elliot argue over a risky decision regarding one of Elliot's patients. Turk tries to talk Carla into entering a practitioner nurse course, so she won't be so underestimated by the doctor's staff.
When an expectant Jordan shows up unexpectedly, Cox is forced to choose between her and his new love, Julie. Meanwhile, J.D. and Turk take advantage of the hospital's supply closet for sleep, when they take on extra shifts at a free clinic to supplement their income. Carla encourages Elliot to stand up to her father, when he pressures her to pick a specialty more "suitable for a woman."
Ever since her father cut her off financially, Elliot's been feeling the weight of the world on her back. While having to find a new affordable place to live, she also has to face the threat of being sued by a patient whom she told he had only eight months to live. Carla and Jordan hit a sore spot when Carla gives her opinion on Jordan and Perry's relationship. Meanwhile, J.D. has a fight with Dr. Cox and the two dispute over who gets to give the better treatment to two patients with the same prognosis.
Elliot still doesn't have a place to live. J.D. think he's lost his mojo when he can't even kiss the giftshop girl while they go out on a date. Turk and Carla are having romance problems, because she feels he's not being as generous to her as she is to him. And Dr. Cox freaks out when he lets Jordan move in to his place due to her pregnancy.
Renewed sex with J.D. calms Elliot, who's facing personal and professional dilemmas: She's broke, and patients are bailing out on her.
Comeuppances are in store for Dr. Cox, Dr. Kelso and J.D. from a hypochondriac, a surgical patient and Elliot, who wants more than just sex from J.D.
J.D. bonds with a patient, who is waiting for a heart transplant and discusses with her their idea of what death must be like. Elliot puts her foot down and demands a feminine locker room from Dr. Kelso. Turk decides it's time to propose to Carla, but a kid swallows the engagement ring.
Turk is still waiting for Carla to answer his proposal and asks his brother to stay over a few days to help him deal with it. Dr. Townshend, an old friend of Dr. Kelso and one of the nicest doctors around befriends J.D. Elliot accidentally finds out the sex of Jordan's baby, becoming the object of Dr. Cox's anxiety.
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.
J.D. and Turk think they've got bad karma after hitting a car and causing an accident, while playing golf on the hospital roof. Dr. Cox bends over backwards to give Jordan as much comfort as possible on her labor day, and she confesses to J.D. that Dr. Cox is the real father. Elliot seeks advice from Carla on how to tell Paul that she's crazy, because they're getting more intimate and she can't hide it anymore. But Carla is feeling too crazy herself with the upcoming wedding.
A personal secret of Dr. Cox is revealed during hospital visitations by a cocky MD (Jay Mohr), who establishes a rapport with J.D.
J.D. flirts with the wife of a patient who's been in a coma for the past two years, whom they all call T.C.W. (Tasty Coma Wife). He feels guilty for doing that, even though she wants to go ahead with it. Meanwhile, he can't stand listening to any more relationship problems, as everybody dumps their issues on his ears: Elliot, sabotaging her relationship with Paul over beef jerky, Carla, finding out her engagement ring passed through a patient's digestive system and Dr. Cox's unsucessful attempts to get some attention from Jordan, who can only think about her baby right now.
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.
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.
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.