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.

J.D. addresses the news that he is going to be a father and Dr. Cox is worried about how his anger is going to impact his offspring. Meanwhile, Carla and Turk prepare for the impending arrival of their new baby. Elliot feels left out because she is childless, while the Janitor wonders if he has wasted his life.

J.D. and Kim start contemplating about their future and their baby's future. Meanwhile, Turk rushes Carla to the hospital after she goes into labor. And Jordan accuses Dr. Cox of not being a more defensive father towards Jack.

J.D. and Kim are surprised of how much they have in common. Recently giving birth, Carla doesn't want to return to work. Meanwhile, Elliot tries to persuade Dr. Turner, a surgeon with thirty years of experience, that medicine is the better option to work with and that surgery could kill him.

Dr. Cox feels like the TV character House when he has to solve several mysteries, one of them being Elliot's anger towards Dr. Kelso, while for some reason she is taking it out on Turk.

J.D. tries to be a better boyfriend to Kim.

Elliot begins enjoying luxuries since she has extra money with her new private practice gig. But eventually, J.D. becomes jealous of her and that forbids him the use of these privileges.

Dr. Cox and the Janitor become roommates in one of the hospital suites, while Turk tries to convince Carla that she has postpartum depression and that she needs help.

After being convinced to go to Tacoma for Kim's first ultrasound, J.D., along with Carla, Elliot, Janitor, Keith and Ted, takes Kelso's new RV on a road trip. Meanwhile, Jordan and Dr. Cox have trouble when Jordan's ultrasound reveals that the baby will need surgery.

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.

J.D. and Turk go to a medical convention in Phoenix, Arizona, where they run into J.D.'s ex-girlfriend Dr. Kim Briggs, who has a surprise for J.D. Meanwhile at Sacred Heart, the janitor pretends to be the chief of medicine and Dr. Cox starts to put doubts about the wedding into Elliot's mind.

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.

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.

Kim goes into labor, and J.D. struggles to decide if he should tell her what he really thinks of their relationship. Turk, desperate to do something not baby-related, races to beat a video game before Carla discovers him. And Dr. Cox searches for someone he trusts enough to give his daughter a shot.

Things get weird for J.D. when he discovers the identity of Kim's new man as he plans to reach out to her in order to move closer to Sam. Meanwhile, Turk starts a campaign for a promotion.

Change doesn't come easy for the gang when J.D. considers moving closer to his son. Meanwhile, Turk gets comfortable as chief of surgery, while Ted and Gooch reach a new level in their relationship.