In the sixth season opener, J.D. deals with the news that he's going to be a father, Dr. Cox worries about how his anger is going to affect his offspring, and The Janitor wonders whether his personal vendetta against J.D. is a waste of time. Also, Elliot decides she too wants children.
A patient hears singing from everyone, turning Sacred Heart into a musical extravaganza. Meanwhile, Elliot determines whether or not J.D. should move in with her, and Carla determines whether or not to go back to work.
Dr. Kelso's thoughts narrate this episode in which he takes a special interest in a patient who is an Iraqi War veteran. The presence of the veteran brings about a political debate amongst the staff regarding the War.
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.
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.
Dr.Kelso's friend is admitted in the hospital but what he doesn't know is that she doesn't have any insurance.He also notices that the staff is stealing scrubs from the hospital.Meanwhile Carla is being blackmailed by the janitor.
Laverne was in a car accident and is in a coma. Everyone has a hard time dealing with it. Jordan is having her baby, but Dr. Cox doesn't want everybody knowing about it. J.D is the only one who knows about the birth and is obsessed with becoming 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 "mack" it with Melody.
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 unbeknown to him the Janitor takes on the role of Chief of Medicine back at Sacred Heart.
Kim moves in with J.D. in order to raise their child together. J.D. learns from Turk and Dr. Cox that fatherhood changes the way of how to see things. Carla complains to Elliot about her being a control freak when they prepare the bachelorette party.
In the season finale, J.D. and Elliot start thinking about their future and if they both made a mistake in not being with each other. The Janitor activates the "Brain Trust" to come up with the perfect wedding gift for Elliot.