The staff at Sacred Heart returns for a sixth season and JD is still reeling from the news that he is going to be a father. Meanwhile, Dr. Cox while readying himself for baby number two, realizes that his constant anger may have future repercussions.
Carla goes into labor and an excited Turk strikes up the band, while escorting her to the hospital, but he still feels upstaged by Elliot's attempts to make Carla more comfortable.
J.D. finds that he is quite compatible with the woman who is the future mother of his child. Turk gets nervous when Carla starts thinking about not returning to work now that their baby has been born. While Dr. Cox continues torturing Elliott, she contemplates moving into private practice. The Janitor leads a strike of the support staff to convince Dr Kelso that they need dental insurance.
Dr.Cox channels TV doctor 'House' to solve three mysteries including: why a man's skin is inexplicably orange; why a young woman, with no coronary issues has a failing heart; and why Elliot is taking her anger towards Dr.
Elliot enjoys pimping out the apartment with the extra money from her new private practice gig and J.D. is enjoying the spoils, but when his jealousy surfaces he loses his new 60-inch plasma TV privileges.
Sacred Heart is turned into a full scale Broadway stage when Patti checks in complaining of hearing incessant music. While trying to determine the cause of this strange complaint the residents of Sacred Heart star in their own musical.
While the staff questions Dr. Kelso's commitment to the hospital we begin to see the world from his point of view. But when he befriends patient, Private Brian Dancer, the war stories he brings back from Iraq remind Kelso what it means to be a good leader.
Turk convinces J.D. that he needs to go to Tacoma for Kim's first ultra sound -- which results in an impromptu road trip for the Sacred Heart crew. After commandeering Dr. Kelso's new RV Eliot, Carla, Keith, Ted and the Janitor join the father to be on his journey. Meanwhile, Dr. Cox and Jordan face some concern when her ultrasound reveals that their unborn child will need to have surgery.
When J.D. develops vasovagal syncope, a condition which results in fainting or blackouts, he finds himself not only having to deal with losing his girlfriend and his apartment, but also his consciousness when pooping. Eliot and Turk debate over whose turn it is to take care of the always down on his luck resident, while Carla tries out her new excuse "I have a baby." Elsewhere, the Janitor embarks on a cruise vacation...or does he?
J.D. falls for a sexy new physical therapist but because of his unfortunate circumstances he finds it difficult to ask her out. Meanwhile, Turk breaks his arm and Dr.
While trying to help a patient regain his memory, the staff looks back on past events. Turk, Elliot, J.D., Dr. Cox, Dr. Kelso and Janitor take a trip down memory lane.
The day has come for Private Brian Dancer to be released from Sacred Heart, but when the military informs him that his injuries are too severe to return to service, he spirals into a state of depression. Eliot, J.D. and Turk rally around him to boost his spirit. Meanwhile, Dr. Cox informs Carla that her jokes are just not funny.
Dr. Kelso doesn’t know it, but J.D. and Turk are trying to beat the system in order to treat the Chief’s uninsured friend. Carla is being blackmailed by the Janitor, while Dr. Cox tries to convince Elliot that a recovering drug addict may not be as clean as she thinks. All the while the entire staff is condemned to wearing brown scrubs after Kelso suspects there may be a clothing thief.
J.D. and Turk try to forget that the Turk's new nanny is smoking hot, but when the pair holds a public screening of the footage from the nanny cam Carla soon catches on.
The staffers deal with the possibility of losing one of their own who is gravely ill in differing ways: Turk and J.D. pull childish pranks while Elliot and Keith spend time together in the bedroom. Meanwhile, Cox and Jordan welcome their new baby, and J.D wants to be named the infant's godfather
After saying goodbye to Nurse Roberts, the Sacred Heart staff institutes some of her lessons into their lives. Though Carla thinks they've all forgotten, Dr. Cox takes time to reflect on his purpose, Elliot opens her heart to Keith and J.D. and Turk learn compassion.
Ted juggles fantasies in which he has a full head of hair and a reality where he is helping the nursing staff fight for a raise. Meanwhile, Todd meets his future son and helps Turk preserve his professional reputation and Jordan puts aside her knack for causing misery to help Elliot and Keith's relationship.
J.D. feels a little left out when Elliot's wild sorority sister, Melody comes to town. Not able to deal with being the third wheel he turns the girls against each other in the hopes that he will once again be Elliot's priority friend and, if he is lucky, that he might get to "mash" it with Melody.
When Elliot's engagement ring does not fit, Keith agrees to a "redo" in which the particular Doctor plans her own engagement. Carla, Jordan and Elliot's sorority sister Melody gather to help plan the "surprise.
As Eliot begins to plan her wedding with Keith, J.D. continues to question his true feelings for her. In an attempt to ease his best friend's mind, Turk takes him to a surgeon's convention in Phoenix, but the plan backfires when J.
Father-to-be J.D. invites mother-to-be Kim to move in with him so that they can raise their child together. Elsewhere, Carla helps Eliot plan for her upcoming wedding, while the Janitor and the "Brain Trust" vow to make Keith the perfect husband-to-be.
The wedding doesn't seem meant to be, when at the baptism for Dr. Cox's daughter the father-to-be and the bride-to-be begin to contemplate the paths they have chosen and question whether or not they were the ones that were meant for each other all along. Elsewhere, Turk learns that life changes when you become a father.