Cox and Kelso still have some issues since Cox punched him a week earlier, and Kelso is still squeaking. Although JD is now starting with the third year; he still needs Dr. Cox's help identifying a patients problem, so the four of them do every single test trying to figure it out. Elliot has some issues with her self confidence, so she buys a car, she meets Sean again, and she goes into a transformation moment that changes both her looks and behavior, so she provides some big help to JD in his patient's problem.
Turk and Carla set a date for the wedding, so JD wants to take Turk out for dinner to celebrate the end of an era, Turk has a problem with being straight with is feelings, until he sees a gay couple in the hospital. Carla finds a urine sample without a tag; she tries to find its patient. Elliot and Sean are back together but starting things up again is really hard because Elliot has a problem finding time for him, because of her job.
Sean isn't happy to hear that Elliott & J.D. have been intimate. It does, however, make it easier for him to break some news to her. Cox applies for a promotion. Jordan hires a babysitter. Carla embarrasses Turk in front of other surgeons.
Carla's brother who hates Turk comes for a visit. J.D. tries to get over Elliott when he meets Danni who *seems* nice. Cox asks J.D. to back him up in front of others. Kelso declares a policy Cox disagrees with. Will J.D. be loyal to Cox?
JD is dating Danni -Jordan's sister- and that means spending more time with Cox outside the hospital, and Perry doesn't very much like it. Danni tells JD that she is falling in love with him, but gets mad for the fact that he wasn't even listening, and while Jordan explains that even they are doctors they don't listen. When that happens, both JD and Cox realize that the patient -that they didn't know what's wrong with- actually tried to commit suicide.
The janitor has three personalities. No, actually four, or five. Cox and Carla get satisfied with their conditions. The first is getting old and Carla's marrying someone who goes to the arcade. JD and Elliot get a little bit competitive.
After Elliot gives a patient an orgasm during a pelvic exam and refers to patients 'private areas' using non-medical terms Dr. Kelso taunts her. Carla tells Turk that she doesn't think they should have again until their wedding night, the Janitor uses this information to his advantage to get back at Turk. Dr. Cox moves in with J.D. and Turk temporarily as a result of not being able to handle his relationship with Jordan.
Danni will move in -temporarily- to JD's. Carla and Elliot find out that a dying patient is still a virgin, and she wants to have sex before she dies, so they go out to find a man-whore. A patient of Perry's is getting a new liver, but Turk gives the opinion that the patient can't have the liver because he drinks.
JD tries to break up with Danni, but he never broke up with anybody. While Perry -for the first time in a long time- is happy, and that reflects on his behavior in the hospital. Now he has the problem of not having anybody interested in his lessons and teaching because the only way he can teach is through fear, so he will have to "scare them back to him". And Elliot finds out that the whole hospital -except the janitor- is making fun of her new look, and she has to lose it or not worry what they think.
Dr. Kevin Casey the medical attendant AND surgeon comes to the hospital to impress them with his extraordinary medical skills, and his severe obsessive compulsive disorder case He gives JD a hard time about his eternal search for a mentor He shocks Turk with his extraordinary surgical skills And takes Cox's position as the greatest-doctor-in-that-hospital
JD and Kevin Casey find out about the roof toilet -aka- the epiphany toilet- Elliot needs help regaining her intubating skills, so she turns to KEVIN CASEY who helped everyone else And Turk asked JD to be his best man, so will JD be the best best man?
It's Jack's first birthday, so Jordan's siblings Dani and Ben are in town. Dr. Cox tells JD to leave a patient for 1/2 an hour and check-up on Ben's leukemia, but when a patient dies, Dr. Cox blames JD, and takes over his patients. Carla and Turk argue about Turk getting rid of his mole and Carla taking Turk's last name. The main theme is acceptance.
It's a battle of the sexes when new female surgeon Dr Miller accuses Turk of being a 'sly sexist' and causes Elliot to question where exactly she stands in the feministic world. Carla is asked to teach a compulsory sexual harassment class with a few surprise students and a few not so surprise students. Meanwhile J.D inspires to help Dr. Cox grieve over his loss by asking Jordan's 'harpie' girlfriends to leave his house.
JD and Carla are becoming closer; furthermore, they are "bead friends". Dr. Ramirez, someone Carla used to like before he left the hospital, is back in town, and Carla goes out with him, not telling Turk. The janitor is dressing up as his "twin" brother, Roscoe, to trick JD and Turk, but they won't fall for it.
JD dresses like a clown to fill into Elliot's shoes. Dr. Cox tries to have the hot Dr. Miller on his side in the war with Kelso. It's Turk's turn to take the narration -since JD is a clown and has nothing to say- and he is afraid of sending the invitations that mean that his wedding is finalized and there is no going back. But Carla makes him know that she is the right person to be with.
Sean comes back and takes Elliot from JD. JD goes back to Danni. The janitor works now as a security guard. Cox finds out that he has a crush on Dr. Miller and is tormented between his crush and his new happy family.
Cox is furious with Kelso for launching a lucrative "body scan" service at the hospital. Carla is becoming increasingly frantic about her impending marriage to Turk. Elliot is about to let Sean move in, but breaks up with him after J.D. confesses his love for her.
J.D. wakes next to Elliott, with the chilling realisation that he doesn't actually love her. At the dress rehearsal for the wedding, Turk is tricked into a humiliating gaffe by Carla's brother. J.D. chooses that moment to come clean with Elliott - who responds by throwing him across a table. Elsewhere, Cox deliberately provokes an argument with Jordan to maintain the spark in their relationship.
Turk and Carla's wedding causes tension between guests, especially Elliot and J.D., whose relationship had taken a nose-dive the week before. Turk attempts to work a little later to have an extended honeymoon, but will he make his big day on time?