Attending at Sacred Heart, J.D. now has to deal with his own interns. Turk has doubts having children, then tries to prevent Carla from getting pregnant. Meanwhile Elliot struggles to find her way at County Hospital and doesn't want to seem like the helpless person she was before.
J.D. wants to show Dr. Cox and Dr. Kelso how to treat interns, but instead he finds out that they laugh at his bad jokes out of fear and respect. Everyone at the hospital is avoiding Jordan to get rid of her except for Turk. An aborted attempt to bond with her results in Jordan being conned by Sam, the drug addict. Elsewhere, Elliot's fellowship goes sour and she finds herself confiding in loose-lipped Carla.
While planning his birthday, J.D. finds a list of things he wanted to accomplish, before he turned 30. He enters a triathlon to begin. Meanwhile, Elliot discovers a side of her boyfriend Jake, that freaks her out. And Turk is working hard to impress his bosses and takes on a patient, who wants to be hypnotized during surgery in effort to be promoted.
J.D. is asked to introduce Dr. Kelso at an awards dinner, so he wants to find out something good about him. Dr. Kelso and Dr. Cox each have a patient, whom they feel deserves the benefit of a new experimental treatment, but there is only one open slot. Elsewhere, Carla and Turk try to help Elliot get her old job at Sacred Heart back. And the Janitor taunts J.D. with the made up game of "Jiggly Ball."
Dr. Cox's religious sister Paige comes to visit for her nephew's baptism. Turk is finding out, just how unsexy baby making can be. Elliot helps him realize that Carla finds the whole process to be romantic. Elswhere, J.D. and the Janitor start a buddy friendship.
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.
In a "Wizard of Oz" homage, J.D. is trying to go home, Turk searches for a heart donor and Carla worries, that she doesn't have the courage to become a parent. Meanwhile, Elliot doesn't believe, that she has the brains to lead a question and answer session. Also, the Janitor is painting color coded lines throughout the hospital for easier navigation.
J.D., Turk, Elliot and Carla are interrogated about the mysterious death of a patient. Dr. Kelso learns, that J.D. and Turk were away tracking down a patient, Elliot was traumatized over finding out that her make-out buddy was married and Carla was busy recruiting hospital personnel for a group lottery purchase.
J.D. meets the klutzy Julie, and when he becomes smitten, Elliot attempts to help out with romance advice. Meanwhile, Carla tries to find Dr. Cox's soft side, when he refuses to kiss his son. Turk and the Janitor put together an air band to win a contest, but Kelso gives them a tremendous obstacle.
J.D. is annoyed that Julie doesn't laugh, so Elliot encourages him to tell her his feelings, as Turk tries to use psychology to fix the issue. Meanwhile, Carla is upset when the Janitor refers to a new nurse as a "hot young Carla," which intensifies her growing concern that she is too old to conceive.
J.D. is still dealing with his recent breakup and trying not to kill intern Keith, who has become annoyingly perfect. To make matters worse, a favorite patient is in a serious coma and each of the staff finds their own way to deal with it. Dr. Cox and the Janitor bond over drinks at the bar and Carla makes it her mission to make the hospital's gym female friendly. Meanwhile Turk suggests, that J.D. and Elliot find themselves 'booty calls'.
Dr. Kelso is outraged, when he discovers, that a bird has been living in Sacred Heart. He orders the Janitor to dispose of it immediately. However, the Janitor likes the bird so much, he secretly keeps it as a pet. Meanwhile, J.D., annoyed with Keith, tries to get his intern fired, but things don't turn out as intended.
J.D. and Dr. Cox go through the five stages of grief with their favorite patient, who is declining in health. Carla forces Turk to go on a string of double dates, including Elliot and her booty call Keith. Elsewhere, Dr. Kelso hits Ted with his car, thus Ted finally has the upper hand with a potential lawsuit.
J.D. is sick of perfect intern Keith and he's not the only one. Elliot's relationship with Keith is revealed, so the other interns think that he is getting special attention. In the meantime Dr. Cox boasts about being named "The Best Doctor in the City" by a local magazine, thus Dr. Kelso assigns him to the most difficult patient in the hospital to deflate his ego. Also, Turk and Carla continue to struggle in their quest for conception.
J.D. urges Cox and his fellow doctors to do special, unconventional things for their patients, but J.D. himself is not sure he can shave his head for a woman undergoing chemotherapy, after meeting a woman who loves his hair. Meanwhile,Turk and Carla attempt to eliminate all the stress in their lives, to better their chances of conceiving. Also, Elliot can't stop giving her new boyfriend Keith stupid gifts.
Turk finds out, that Carla is pregnant, before she does, so J.D. convinces Turk to tell the entire hospital staff to surprise Carla with the news. But Carla wants to personally share her baby news with everybody, so Turk and J.D. have to quickly contain the hospital gossip. Meanwhile, when Elliot puts Dr. Cox into an embarrassing situation, he decides to get even with Elliot through Keith and Carla.
When J.D. rearranges his schedule to allow himself more time to spend with Turk, Turk secretly resents hanging out with J.D. in that time because it interferes with his own "Turk Time." Meanwhile, Dr. 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.
J.D.'s brother Dan returns for a surprise visit and Elliot learns that J.D. has been telling Dan that she still likes him. A patient with weight-related problems needs an MRI, but he's too big for the machine. Carla and Turk freak out when they begin to discuss baby names. Meanwhile, Dr. Kelso assigns Dr. Cox to assist Ted with malpractice claim paperwork after Dr. Cox insults Dr. Kelso's son.
Turk and Carla turn J.D.'s old bedroom into a nursery for the baby. The Janitor seizes an opportunity to shove J.D. out of the picture for a day. Elsewhere, Elliot uses her mother to learn information about Keith's peers and Turk & Dr. Cox accuse each other of not being hip.
J.D. asks Dr. Cox out for lunch, but runs into annoying former patient Jill Tracy, who unexpectedly teaches him something about responsibility. Elliot and Carla discover that Todd has been lying about all his hospital "conquests" and suspect that he's been less than truthful about other issues. Turk warns them not to meddle in his affairs.
Dr. Cox starts drinking after his decisions result in the death of three of his patients. The staff tries to cover for him at the hospital, while everyone tries to convince him how inspiring he is for them. Turk starts his new rotation with orthopedic surgery, but isn't so fond of his attending doctor's touchy-feely methods. Thus, J.D. and the Janitor attempt to help Turk find ways to bond with his new supervisor.
J.D. feels that the same things happen over and over again at the hospital. Dr. Cox returns to work, but Elliot believes that he has lost his usual confidence. Elliot calls Dr. Cox on his behavior. Carla gets fed up with Turk, because he still can do a lot of stuff, but she can't since she is now pregnant.
J.D. challenges an urologist's assessment on a consult for a patient in need of a risky surgical procedure. He also starts to fall for her. Meanwhile, Elliot considers breaking up with Keith, but Carla is showing extreme hormonal changes due to her pregnancy and tries to interfere. The Janitor and Dr. Kelso are having a little tiff of their own about fear.
J.D. plans a date with Kim on their night off but Elliot keeps getting in their way. Meanwhile, Elliot throws a baby shower for Carla.Perry and Jordan hand over all of Jack's stuff to Carla. And someone announces a very surprising pregnancy.