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?
As Turk and Carla return from their honeymoon, J.D. prepares for his first day as a qualified doctor. Elliot is still infuriated with him over their break-up. The hospital has a new psychiatrist, the somewhat dippy Dr Molly Clock. Dr Cox warns J.D. he still has much to learn.
Elliot, who thinks of Molly as her mentor, finds out that she isn't perfect. Carla gets tired of Turk waking her up when he enters the bedroom and enforces a bedtime on him. J.D. loses what little respect of his residents he had.
J.D. makes-out with Molly at her going-away party. He then gets approval from Elliot to sleep with Molly before she moves away. Dr. Cox has to complete community service in an ambulance with a Paramedic who talks endlessly.
J.D. takes matters into his own hands, when searching for a relative for his favorite patient. Meanwhile, Elliot is fed-up with co-workers not taking her seriously, and discovers she can get her way by flaunting her femininity with some help from Carla and Jordan.