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.

A run-in with her old flame Sean and an accident in her new car lead Elliot to the realization that nothing good has happened to her in the three years that she has been at Sacred Heart. This realization drives her to take drastic measures, including a complete makeover, both inside and out, in an attempt to change her luck.

Meanwhile, J.D. gets stuck with a patient, whose diagnosis he can't quite pin down, and when Dr. Cox denies him any assistance, he looks to Carla and Turk to help him out. While Dr. Cox is busy not helping J.D., he takes the time to make amends with Dr. Kelso.

J.D. is feeling left out of his friendship with Turk and gets hurt when Turk is scared of opening up to him.

Meanwhile, Carla is driven crazy over an unidentified urine sample, and Elliot tries to balance Sean and her career, so that one doesn't end up getting in the way of the other.

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.

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.

Dan decides to stay with J.D. for a while after their mom's new fiancé kicks him out, but after spending some quality time with him at the hospital, Dan isn't sure if he likes the cynical person his little brother has become.

Elliot tries to deal with her own problems of a long distance relationship and decides to try moonlighting as a pet examiner with Carla to save up money.

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.

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.

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.

Carla and Elliot try to help a patient, Maggie, lose her virginity as she prepares to die.

Walking in on her sister and Dr. Cox prompts Danni to move in with J.D. Dr. Cox attempts to convince Turk to do a kidney transplant for a patient he has "moved up" the list. But a personal grudge seems to stand in the way and may decide whether the patient lives or dies.

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.

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.

Jordan's friends Allison and Maddie come to town to provide moral support for Jordan after her brother's death – however, their constant presence does not provide any relief to Dr. Cox.

Meanwhile, Turk tries to impress the new female surgeon, Dr. Miller, but his first encounter serves only to leave him baffled by the opposite sex yet again. Attempting to reinforce the policy on sexual harassment at Sacred Heart, Carla is forced to teach a course where Dr. Kelso is the number-one student.

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.

J.D. must keep a secret when Carla's "what-if" guy asks her out on a date.

Meanwhile, on the other side of the argument, Carla hounds Turk for checking out other women.

Elliot is also on the spot as Dr. Cox and Dr. Kelso both advise her not to give her patient drugs as they suspect he is an addict faking pain.

Turk has to confront a young patient of his, when he accidentally cuts a nerve and the boy (who happens to be a concert pianist) loses use of one of his hands.

Meanwhile, one of Elliot's patients unintentionally teaches her a lesson about her relationship with J.D.

J.D. hooks up with Danni again, after Sean returns, but he can't forget about his passionate night with Elliot.

Meanwhile, Dr. Cox realizes, that he might actually have a crush on the one doctor he loathes.

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.

J.D. is unsure what to do, when he realizes he made a mistake telling Elliot he loved her.

The Janitor squares off against Dr. Cox after he loses the election of the janitors to Randall.

Carla's brother Marc constantly puts Turk in a tough situation, when Turk forgets to write his wedding vows.

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.