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. Elsewhere, Turk and Carla prepare for the arrival of their little one, while Elliot laments that she is the only one in the hospital not having a baby! They all begin to see a little of themselves in their patients ailments, but will they find the cures?

Carla goes into labor and an excited Turk strikes up the band -- literally -- while escorting her to the hospital, but he still feels upstaged by Elliot's attempts to make Carla more comfortable. A scheme to make himself look like the hero backfires and Turk is in jeopardy of missing the birth of his child. Lucky for him the whole thing is mistakenly being broadcast over the hospital's closed circuit TV. Meanwhile, J.D. and Kim contemplate their future and the future of their child.

The expirienced surgeon Dr. Turner is going to lay down on the operation table. Elliot tries to convince him that medicine is a better option since surgery could kill him.

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. Kelso out on Turk. But the doctor may be missing the biggest clue of all when Carla begins to show signs of postpartum depression. Meanwhile, J.D. tries to be the 'best boyfriend ever' so that Kim won't take the job in St. Louis

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. Elsewhere, Dr. Cox, in an attempt to hide from Jordan, bunks with the Janitor in one of the hospital's luxury suits - but the happy roommates soon turn on one another and their rivalry escalates until only Dr. Kelso (Ken Jenkins) can save them. Meanwhile, Carla is still struggling to admit that she may have postpartum depression and Turk encourages her to seek help.

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. Carla and Turk tango over her decision to be a stay at home mom or to return to work, while Elliot struggles with telling J.D. that she doesn't want to be roommates with him anymore.

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 begins back from Iraq reminds Kelso what it means to be a good leader. Meanwhile Dancer's presence in the hospital causes a heated political debate amongst the staffers dividing them down party lines, while everyone is fighting the patient's well -being is being neglected. Elsewhere, J.D. is in search of a new apartment and feels out of the loop when politics becomes the topic of the day Sacred Heart.

Turk convinces J.D. that he needs to go to Tacoma for Kim's first ultra sound --which results in an impromtu road trip for the Sacred Heart crew. After commandeering Dr. Kelso's new RV Eliot, Carla,Keith, Ted, and the Janitor and the father to be on his journey. Meanwhile Dr. Cox and Jordan face some concern when her ultrasound reveals that her 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. 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. Kelso sends him back to residency where, with the help of Dr. Cox, he realizes that he knows less about actual medicine than he thought he did. Elsewhere, Eliot invites Keith to move in with her, but isn't quite ready to compromise her house rules. All the while Carla provides each of the doctors with guidance while they get over their fear, ignorance and stubbornness.

While helping a patient regain his memory, the staff at Sacred Heart stir up some memories of their own. J.D, Elliot, Turk, Carla, Dr. Cox, Dr. Kelso and Janitor take a trip down memory lane in this unique look back on six years of 'Scrubs.'

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.

Unbeknown to Dr. Kelso, J.D. and Turk try to beat the system to treat the Chief's uninsured friend. Elsewhere, the Janitor blackmails Carla with a case of mistaken dog identity. Meanwhile, Dr. Cox tries to convince Eliot that a reformed drug addict isn't quite clean. All the while the entire staff is condemned to wearing dirt brown scrubs when Kelso suspects a clothing thief in their midst.

Turk hires a hot nanny and though both Turk and J.D. are pleased with her, Carla is not. Elliot and the Janitor due their best to cheer up a dying patient, but Dr. Kelso isn't thrilled with their enthusiasm. Meanwhile, Nurse Roberts and Dr. Cox debate whether or not everything happens for a reason.

Nurse Roberts' condition begins to worsen and each of the staff members deal with the possibility that she may not make it in their own, individual way. Elliot and Keith cope by staying busy together, J.D. and Turk deal through childish behavior, and Carla finds comfort in an unlikely source. But as one life may end, Dr. Cox and Jordan welcome a new life and J.D. tries to sell himself as the best choice for the baby'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.

In a unique twist, J.D. turns his narrating duties over to Ted, Todd and Jordan -- as this episode focuses on the lives of the supporting players at Sacred Heart Hospital. 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; Todd meets his future son and helps Turk preserve his 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 Eliot'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 Eliot's priority friend and, if he is lucky, that he might get to mash it with Melody. Meanwhile, Turk and Dr. Cox go head to head when they disagree over whether or not a patient requested surgery is necessary. Elsewhere, Carla discovers an unlikely ghost haunting pediatrics in an attempt to keep it clean. In the end one of Sacred Hearts own will be considering a marriage proposal.

When Eliot's engagement ring doesn't fit, Keith agrees to a redo in which the particular Doctor plans her own engagement. Carla, Jordan and Eliot's sorority sister Melody gather to help plan the surprise. Meanwhile, the men of Sacred Heart are suffering from too much talk and not enough action as J.D. continually gets shot down by Melody, Turk and Carla have not been intimate since their baby was born and Dr. Kelso's cold showers. In the end J.D. realizes that he might still have feelings for Eliot.

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.D. runs into his ex-girlfriend Kim and comes face to face with the unexpected. Meanwhile, Kelso and his cronies party it up at the convention while unknown to him, the Janitor takes on the role of chief of medicine back at Sacred Heart.

JD struggles to decide whether he will forgive Kim and stay with her or not and Carla struggles to prepare a party for Elliot, who proves to be an enormous control freak.

The christening of baby JD, Dr Cox an Jordan’s daughter, is all that JD can think about until they replace him as godfather. Elliot has doubts about her marriage with Keith, who is being lectured by the brain trust on how to be a good husband. JD still has doubts about his relationship with Kim and he and Elliot end up in the on call room all alone.