John Dorian, "J.D." to friends, is a boyishly handsome, self-deprecatingly funny, likeable guy who would be confident if he only realized his assets. Four years of medical school have prepared J.D. for his first day as an intern at Sacred Heart Hospital - but he has his doubts.

J.D. and Turk's college buddy, Spence, drops by for a visit, and accidentally tells Dr. Cox a secret. Too much partying with successful Spence causes Turk and J.D. to show up late and drunk for work, which Dr. Kelso fully reprehends them for. Elliot's feeling low since she can't measure up to Dr. Kelso's standards, and the Janitor starts another feud – this time over paychecks – with J.D.

A run-in with her old flame Sean and an accident in her new car lead Elliot to the realization that nothing good has happened to her in the three years that she has been at Sacred Heart. This realization drives her to take drastic measures, including a complete makeover, both inside and out, in an attempt to change her luck.

Meanwhile, J.D. gets stuck with a patient, whose diagnosis he can't quite pin down, and when Dr. Cox denies him any assistance, he looks to Carla and Turk to help him out. While Dr. Cox is busy not helping J.D., he takes the time to make amends with Dr. Kelso.

The big day for Turk and Carla has finally arrived, but a patient holds up Turk.

With Elliot still angry at him, J.D. attempts to reconcile her with Sean as a way to make everything right again in their friendship.

Turk and Carla start to have issues when Carla tries to change everything about her new husband. Molly Clock (Heather Graham), the hospital's new psychiatrist, becomes friends with Elliot because she believes Turk, J.D. and Carla are shutting her out. Also, when Turk and J.D.'s car blows up, Carla lets him pick out the new ride only to find that instead of a car, he buys three scooters for them, further proving Carla's point that she needs to always be in control. The episode guest stars the Sugarhill Gang.

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.

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.

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.

When Keith leaves town for a few days, J.D. expects that he'll finally be able to spend some quality time with Elliot. But he doesn't anticipate Elliot's old college friend dropping by. J.D. switches between hitting on her and competing with her for Elliot's attention. Meanwhile, Turk and Dr. Cox volley a hypochondriac patient back and forth since there's nothing wrong with him.

In the aftermath of their near-indiscretion, Elliot realizes she doesn't want to be with Keith, and J.D. resolves to stop sabotaging himself.

Meanwhile, Dr. Cox and Turk find a patient they both like who is in danger of being discharged.

J.D's brother Dan returns and delivers a few home truths to his little brother. In the meantime, Elliot and Dr. Cox debate over the morals of their practice and the staff of Sacred Heart find the Janitor's behavior rather odd after he watches "An Inconvenient Truth".

J.D. and Turk make a huge sacrifice concerning a decade-long steak night tradition for a dying patient. Meanwhile, Dr. Maddox, the new Chief of Medicine, begins to show her true colors.

Featuring a special appearance from Sesame Workshop's "Muppets", J.D. learns a lesson about the gift of compassion, while Elliot gets scammed by intern Katie to secure a spot on Turk's team.

The Janitor and Lady invite the Sacred Heart staff to their fake wedding in the Bahamas hoping to score some loot but their scheme is about to backfire...

The tropical seaside wedding goes ahead as the Janitor and Lady tie the knot which affirms the relationship of another couple.

J.D. is planning on leaving Sacred Heart but before he goes there are a few things that he wants to do including; getting a hug from Dr. Cox, and learning the Janitor's real name. Elliot is ready for the next step in her and J.D.'s relationship and she begins moving her furniture into J.D.'s apartment.