Elliot attempts to change her luck with a full body makeover after running into Sean. JD asks for Turk and Carla's help with a baffling patient. Dr. Cox tries to come to an understanding with Dr. Kelso after his punch causes Kelso to have a loud squeaking noise come out of his nose.
JD wants to help Turk celebrate the end of his bachelorhood when Turk and Carla decide on a wedding date, but Turk has to come to terms with sharing emotions with other men. Elliot has to decide how to balance her time between work at the hospital and relationships when she sets her sights on Sean.
JD, Turk and Elliot all get interns of their own and each has a different educational technique. JD gets training advice from Sean. Dr. Cox and Jordan search for a doctor for their child.
Sean is freaked to find out that Elliot and JD were once an item, but it may be a cover to hide that he has a long work trip ahead of him. Cox attempts to become the hospital's new resident doctor. Carla works as a surgical nurse and shadows Turk.
Dan drops in on JD after being kicked out by his mother's fiancee. Elliot tries to handle her long distance relationship with Sean. Carla and Elliot take up night jobs at a veterinary clinic to save money.
A female stranger helps JD process his feelings for Elliot. Carla's brother visits and tangles with Turk. Cox takes over the Resident Director spot.
JD's relationship with Jordan's sister causes him to spend time with Cox. As they work against each other, it only upsets Danni and Jordan. When Kelso accidentally deafens himself, the staff unload their feelings about him.
Turk basks in the glow of a successful first solo surgery and Elliot wonders when she will have her establishing act as a doctor. Cox tries to beat aging through denial when his back goes out. JD learns new information about the janitor.
Elliot has a hard time referring to sexual organs by their proper medical names. JD's patient refuses treatment in fear that it will hurt his sexuality with his wife. Cox puts off sex with Jordan because of time constraints. Carla lets Turk know that she wants to refrain from sex until they are married.
JD worries about his relationship with Danni after he agrees to let her move in for a bit to escape her sister and Dr. Cox. Carla and Elliot try to recruit a man for a dying woman who doesn't want to go a virgin. Turk tries to face down Cox's dislike of him because of Carla's friendship with Cox.
JD's toil over breaking up with Danni is pushed away when Jordan breaks it off on Danni's behalf. Cox finds his residents lack the proper amount of fear since he's become a caring parent. Elliot tries to prove that her looks don't affect her ability to be a doctor.
Sacred Heart receives a visiting surgeon with obsessive compulsive disorder. He knocks Turk off his throne for fastest surgery and JD tries to turn to him as a mentor. Kelso and the Janitor come to terms with disposal of the hospital's garbage.
Elliott questions her abilities and turns to Dr. Casey for help. JD feels slighted when he learns that Turk asked his brother to be best man before turning to JD. The Janitor's secret rooftop toilet gets a lot of attention from the staff.
Cox has JD run tests on Jordan's brother who has been out of the country since he beat back leukemia. Elliot's foot problem leads to a confrontation between Carla and Turk.
Jordan's friends visit to support her through dealing with her brother's death but tax Cox's patience. Turk has problems dealing with the new female surgeon. Carla tries to educate Kelso in the area of sexual harassment.
The results of a day at the hospital are greatly affected by a butterfly's decision to land on the chest of a beautiful and curvy woman or a slightly unseemly man.
Carla is tempted by a fruit other than Turk when an old colleague comes to town and asks her out to dinner. JD gets caught in the middle when Carla makes him swear he won't tell Turk. Elliot fights for a patient even though Cox believes he is a fake in search of drugs. JD and Turk make the acquiantance of the Janitor's supposed twin brother.
JD takes over for Elliot as the Kids Day clown and seemingly wins her heart over until Sean arrives out of the blue from New Zealand. Turk worries about sending out the wedding invitations and is only reassured by the fact that Carla really knows him and loves him. Cox and Kelso battle over a female surgeon.
Carla and Turk try to help JD through the return of Sean into Elliot's life just after JD and Elliot shared a passionate exchange. Danni comes back into JD's life and Cox tries to figure out his own feelings with regards to Dr. Miller. The Janitor takes up the role of the Security Guard at the hospital.
JD and Danni end things because JD still cares for Elliot. JD decides to step up to the plate when Elliot asks Sean to move in. Cox and Kelso debate the hospital's need for body scans and Turk and Carla start to freak out as their wedding day approaches.
Turk faces an uphill climb to his wedding day when he forgets to retrieve Carla's brother at the airport and gets wedding vow writer's block. JD seeks advice in how to break the news to Elliot that he doesn't love her. When Jordan stops fighting with Cox, Cox turns to the rest of the hospital staff to fill the void.
Turk's extra shift at the hospital leaves Carla stranded alone at the alter as the anxious crowd grows unruly. JD tries to patch things up between himself and Elliot by attempting to get her back together with Sean.