Life has changed. J.D. is now an attending and has new interns to guide, but still lives in his old apartment, hiding from Carla. Elliot tries to project a confident image at her new job. Turk's trying to get Carla pregnant. Or is he?
Elliot has an annoying new colleague. Cox needs a break from Jordan and orders her to find friends at work. Carla gets the impression that Elliot is ashamed of her "old" colleagues. J.D. realizes his interns find his jokes unfunny.
Carla's still the only one who knows Elliot's fellowship was canceled. J.D. is turning 30 and gets the urge to achieve something. Turk is fighting for an attending's spot. Elliot wants Jake to open up but isn't prepared to handle it.
J.D. has to introduce Kelso at an awards banquet--a job made more difficult when he rejects a patient for a drug trial in favor of a richer patient. Meanwhile, the guys want to try to get Elliot's job back.
J.D. mistakes an elderly woman's happiness as her wish to stop treatment for a fatal illness. Turk and Elliot struggle to find the cause of a patient's body pain and Carla tries to organize the annual group photo.
One hundredth episode. As a tribute to "The Wizard of Oz", the four companions go on a similar journey. Turk needs a heart from a patient in order to be the first resident to assist performing an in-house heart transplant. Carla needs courage to have a child with Turk even though she can't stand babies. Elliot needs the brains to handle speaking in a medical seminar. And J.D, well, he just wants to get home...
When a potential new girlfriend enters J.D.'s life, Elliot offers J.D. relationship advice and tries to help break his bad habit of ruining romantic moments by uttering really inappropriate things. Meanwhile, Jordan and Carla each have problems with Dr. Cox, and Turk joins the hospital air band.
When Carla begins to feel old, she drags her friends to a college club and decides to take a fertility test, among other things. And while all of J.D.'s friends love Julie, they begin to worry that J.D. is going to ruin the relationship after he begins saying his thoughts aloud.
The Sacret Heart staffers each try different ways to take their minds off the fact that a favorite patient, Mrs. Wilk, has to undergo an extremely risky procedure. While J.D. and Elliot try to get lucky in love, or maybe just find themselves booty calls, Dr. Cox finds a new drinking buddy in the Janitor, and Carla encourages Turk to fight for a female-friendly hospital gym.
J.D.'s dislike for and resentment towards intern Keith increases to the point where J.D. tries to get him dismissed from Sacred Heart, but the plan backfires. Elsewhere, Elliot and Turk misplace their patient's deathbed statement to his children; and the Janitor attempts to keep a pet bird in the hospital without Dr. Kelso knowing it.
Grief counseling is offered to Mrs. Wilk, whose condition has worsened considerably. As she comes to accept her fate with help from a quirky therapist, J.D. and Dr. Cox surprisingly turn to each other for support as they face losing their favorite patient. Elsewhere, Ted and the Janitor team up to give bitter Kelso a taste of his own medicine, and Elliot's relationship with Keith changes.
Elliot gets upset with J.D. when he doesn't defend her after she's accused by the other interns of giving preferential treatment to Keith. Meanwhile, Dr. Cox is stuck caring for one of Dr. Kelso's old, miserable, and demanding friends, and Carla resorts to trickery to find out if Turk is sterile.
When Dr. Cox scoffs at reading lines with a patient preparing for a play, J.D. urges his fellow doctors to do special, unconventional things for their patients. But when J.D. scores a date with a hot babe who loves his hair, he's not sure he can shave his head for a woman undergoing chemo. Turk and Carla attempt to eliminate all stress to better their chances of conceiving, but Turk has to compete for a surgical resident spot and Carla loses Dr. Kelso's VIP patient. Meanwhile, Elliot showers Keith with stupid gifts.
When J.D. rearranges his schedule to allow himself more time with Turk, Turk secretly resents hanging out with J.D. because it interferes with his own "Turk Time." Meanwhile, Cox and Jordan go on a double date with Elliot and Keith, and Carla covers for Kelso at work as he grieves for his dead dog. Later, a patient almost dies after giving up part of his liver for his brother, and the hospital staff learns about making sacrifices for the people they really care about.
The hospital is seen from the perspective of The Janitor, who's out to prove he can make a difference after getting rid of J.D. for the day. Also, Turk sees his "blackness" called into question by Dr. Cox, and Elliot's intern's mistakes begin to frustrate her.
J.D. accidentally runs into Dr.Cox in a store, who both then run into annoying former suicidal patient Jill Tracy. Meanwhile Elliot and Carla do a little investigating and find out that Todd hasn't actually slept with anyone in the hospital - they jump to conclusions about his sexuality.
Carla persuades all her coworkers to rally around a despondent Dr. Cox, after three of his patients die because of his mistake. Everyone participates except J.D., who thinks his selfish reaction crossed the line.
Dr. Cox returns to the hospital, but Elliot quickly learns the hard way that he's still his same old obnoxious self. And Carla forces Turk to also give up the things she has to give up while she's pregnant.
J.D. challenges a urologist's assessment on a consult for a patient who might need a risky surgical procedure, feeling that she's playing it safe professionally and personally, since he also starts to fall for her. Along the same lines, Elliot considers breaking up with her boyfriend/intern Keith for being too weak, especially when he's being picked on by Dr. Cox.
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.