After Jordan dropped the bomb that JD and her had slept together, Turk knew that Dr. Cox still likes Carla and the fact that Elliot has feelings for J.D. things are a bit tense at Sacred Heart. Turk and Carla try to deal with the fact that they have trouble trusting each other and J.D. tries to fix both his relationship with Dr. Cox and Elliot, which turn out the be much more difficult than he thought.

It's JD's, Turk's and Eliot's first night all alone and without supervision at the hospital. The night they have all been waiting for, but they soon find out that it isn't as easy as they have imagined it when they are flooded with work which forces them to seek help from Carla, and even the Janitor. Meanwhile, Dr. Cox has agreed to introduce Dr. Kelso at an awards ceremony which he is not looking forward too at all.

To motivate the residents Dr. Kelso announces that the person with the most interesting case study will get to go to a medical conference in Reno which makes all the residents look like crazy to find themselves an interesting case, everyone except J.D.. Elliot and Carla realize that they have more in common than just their relationships with J.D. and Turk, meanwhile Turk is in big trouble as he forgot to ask for a new laser for the surgical team on the one day that Dr. Kelso grants requests.

Elliot's latest try to win points with Dr. Cox has her delivering bad news to patients on Dr. Cox behalf, she thinks it's fine at first, but she soon learns that also she has a limit. J.D. betrays Carla by telling Turk some of Carla's feelings and insecurities towards him, while Turk has been selected to represent Sacred Heart on a trip for the Doctors Without Borders program, but when he finds out that his toughest rival Bonnie wasn't chosen just because she is female he isn't so sure he wants to go.

J.D. gets a reality-check when the white lab coat that he is allowed to wear as a resident does not bring the new level of respect he thought it would, and Elliot earns a reputation after her first one-night stand with another doctor. Meanwhile, Turk tries to fit-in with the surgical boys club and finds himself struggling with whether being part of the club is worth the price of admission. Dr. Cox teaches Carla a lesson about surviving in medicine, by enrolling a patient into a clinical trial without approval.

J.D. gets a surprise visit from his ne'er-do-well brother Dan, and becomes jealous when he and Elliot hit it off. Meanwhile, Turk feels guilty after betting Dr. Cox $20 that surgery would save a patient's life.

Dr. Cox's efforts to take a stand against the evil drug companies are thwarted by the seductive charm of pharmaceutical sales rep Julie Keaton. She takes advantage of the fact that Dr. Kelso has assigned Dr. Cox to coordinate a dinner reception sponsored by the drug company to pursue Dr. Cox in other arenas. Elliot and J.D. disagree about who is the better doctor, but when Elliot disregards his advice about how to treat her patient and the patient dies, it is actually J.D. that learns a lesson about taking chances. Meanwhile, Turk tries to encourage Carla to take her career to the next level by enrolling her in a nurse practitioner course.

Dr. Cox's relationship with pharmaceutical rep Julie Keaton is off to a good start when they wake up together, but when Jordan shows up with a surprise, Cox if forced to choose between the new woman in his life and the ex-wife he can't get out of his life. Elsewhere, J.D. and Turk take advantage of the hospital's supply closet, while taking on extra shifts at a free clinic to supplement their income as residents and Carla encourages Elliot to stand up to her father when he pressures her to pick a specialty more suitable for a woman, especially when it will prove Dr. Kelso wrong.

JD is riding high after correcting a misdiagnosis by Dr. Cox, but is jerked back to reality when he is unable to explain the death of his next patient. Meanwhile Elliot is struggling personally and professionally as she is forced to relinquish all of the luxuries that her father had been financing -- including her apartment -- and a malpractice suit is brought against her by a patient for saving his life. Carla learns that sometimes it is better to keep her opinions to herself when the fallout of a conversation with Dr. Cox about his relationship with his ex-wife lands Jordan in the hospital.

Elliot continues her search for a place to live, JD asks the gift-shop girl out on a date, and Carla has romance problems with Turk. Meanwhile, Dr Cox lets newly pregnant Jordan move into his apartment.

J.D. and Elliot continue to seek relief from their problems by sleeping together, but when things start to get a little out of control, Elliot proposes that they become sex buddies, which seems at first to be the perfect solution. Elliot thinks she has a handle on things, but when Turk is forced to take the heat from Dr. Cox for her mistakes with one of their patients, he tries to lighten her load by suggesting that her patients switch to the care of other doctors. His good intentions put him at odds with both his friends and they are forced to reevaluate their arrangement. Meanwhile, Dr. Kelso accuses Carla of making her relationships with her patients the priority over their well-being.

J.D. wrestles with his feelings for Elliot and can't handle being just friends especially when Elliot needs a friend the most. Meanwhile, Dr. Cox and Carla realize they are not as close as they used to be when they fail to read each other's signals while treating a hypochondriac patient.

Turk makes plans to propose to Carla, only to watch all his plans fall apart when one thing after the next prevents him from actually popping the question. Meanwhile, J.D. comforts a patient in need of a heart transplant by explaining his theory about the balance between life and death in the hospital. This theory is put to the ultimate test when a husband must choose between saving his unborn child and his wife's well-being. On another front, Elliot prevents Dr. Kelso from expanding his office space when she launches a campaign demanding that Dr. Kelso build a separate female locker room.

Dr. Kelso assigns J.D. to work on a patient with Dr. Townshend, but things go downhill when Dr. Townshend insists on using his old school treatment method which proves to be an alien concept to an inept J.D. While Kelso defends his friend's technique, Dr. Townshend's lack of current medical knowledge forces Kelso to admit his mistake. Meanwhile, Carla tells Turk she needs time to consider his proposal because she thinks he is still too immature, prompting Turk to invite his married brother for a visit to show Carla how seriously he is. In addition, Elliot learns the sex of Jordan's baby, but Dr. Cox and his ex-wife can't agree if they want to know.

At a bar, Carla makes a decision on the right answer to Turk's proposal while Elliot thinks she has struck gold when she meets Paul, a charming man whom she recognizes from the hospital and assumes is a fellow physician. However, the next day, she learns that he is a nurse, and she is forced to put her ego in check to give the relationship a chance. In the meantime, J.D. enjoys a rare day when everything goes right while Dr. Cox' world is in chaos as he manages to alienate himself from all of his colleagues at the hospital.

Elliot tries to keep up her perfect persona for her new boyfriend for fear he won't like her if she tries just being herself. At the hospital, things misfire for Jordan and Dr. Cox when a miserably executed practice run of the baby's birth turns into the real thing -- and in the throes of labor, Jordan reveals the identity of the baby's father to J.D. Meanwhile, Turk and J.D. can't handle their guilt when they believe that one of the golf balls they hit off the hospital roof caused a car accident.

While J.D. struggles with whether to tell Dr. Cox the truth about the baby's paternity, he gains some valuable insight into Dr. Cox' troubled mind and his relationship with Jordan when he meets Dr. Fisher, a former student of Dr. Cox. When Dr. Kelso prevents Turk from playing his pre-surgery basketball game, Turk retaliates by cutting the cord to Kelso's beloved Ms. Pac Man machine. Meanwhile, Carla worries that she's lost her sex appeal since she got engaged and Elliot's lucky streak continues as she makes a new friend in the janitor.

When J.D. starts getting flak from his friends about dating a woman who is visiting her comatose husband, he quickly becomes defensive. Elsewhere, Carla and Turk fight over every little thing since they became engaged, Dr. Cox is jealous of all the attention Jordan gives the newborn baby and Elliot overreacts because she thinks Paul doesn't trust her.

J.D., begins a surgical rotation and in an attempt to lose his nerdy medical resident reputation he reveals a secret about Turk to get in with the rest of the surgeons. While his betrayal earns him a place at the surgical table, it may cost him a friendship. Meanwhile a miscommunication between Elliot and Paul leads to confusion about their true feelings for each other and Dr. Cox plays a deadly practical joke on Dr. Kelso.

JD finds himself in a tough spot after a romp with Jamie in a funeral home leads him to an accidental sighting of the janitor's private equipment and a language barrier with a patient results in some major miscommunication. Meanwhile, Turk starts having steamy dreams about Elliot making things a bit uncomfortable, especially when Carla finds out and Jordan forces Dr. Cox to watch her still-to-be-named son.

The unexpected death of Carla's mother causes her to second guess her wedding plans with Turk. J.D. turns to Elliot for help when his romance with Jamie begins to fizzle, and Dr. Kelso appoints Dr. Cox to teach a daily seminar on doctor-patient relations as punishment for his inappropriate behavior.

When J.D. and Turk are paid a visit by their college cohort, Spence -- who is now leading a life of luxury as an investment banker -- they are struck by the daily sacrifices they make as residents leading them to re-evaluate their career choices. Spence's visit also triggers the reveal of another dirty little secret - Dr. Cox learns the truth about his relationship to Jordan's baby, but the truth may be more than he can handle. Meanwhile, Elliot's skills and patience are tested by the unrelenting Dr. Kelso.