Scrubs heads into its fifth season focusing on the strange experiences of medical resident John "J.D." Dorian as he embarks on his career in a hospital where humor and tragedy can merge paths at any time.
J.D. is now an attending at Sacred Heart Hospital. He wonders how his new interns will see the hospital for the first time and the majority of the episode is then in first person view of J.D.’s new intern Keith. Turk sneaks J.D. around Carla and Turk’s house, since J.D. is without a home. Meanwhile, Turk and Carla are trying to make a baby, but Turk has been sneaking Carla birth control pills. At the same time, Elliot has started a new job at North County University Medical Center, but continues showing up at Sacred Heart Hospital to avoid looking foolish at her new job.
J.D. wants to show Cox and Kelso how to treat interns but instead finds out that they laugh at his bad jokes out of fear and respect.
While planning his birthday, J.D. finds a list of things he wanted to accomplish before he turned 30. He begins by entering a triathlon.
J.D. is asked to introduce Dr. Kelso at an awards dinner, so he tries to find out something good to say about him.
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.
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.
J.D., Turk, Elliot and Carla are interrogated about the mysterious death of a patient.
J.D. goes on a blind date with a patient’s niece. He is expecting the worst, but is surprise to find out his date Julie (Mandy Moore) is perfect with the only flaw of being clumsy. Elliot attempt to offer J.D. some relationship advice so that he won’t "ruin the romance" and to not rush things as he always does. Turk joins an air band at the hospital with The Janitor, Ted, and Lloyd the Delivery guy, but when Turk gets on Dr. Kelso's bad side there are repercussions. At the same time Dr. Cox refuses to kiss his son, believing it will make his son soft. Meanwhile Carla is worried about her age because of her failed attempts to conceive.
J.D. is annoyed that Julie doesn't laugh, so Elliot encourages J.D. to tell her his feelings and Turk tries to use psychology to fix the issue.
J.D. is still dealing with his recent break-up 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. 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. J.D., annoyed with Keith, tries to get his intern fired but all doesn'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.
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 he is getting special attention.
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 chemo after meeting a woman who loves his hair.
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.
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."
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.
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.
J.D. asks Dr. Cox for lunch but runs into annoying former patient Jill Tracy, who unexpectedly teaches him something about responsibility.
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.
Dr. Cox returns to work, but Elliot senses he isn't the same. It seems as if he lost his confidence. J.D. is getting the feeling that he has experienced some of the events happening before. Meanwhile, Turk is enjoying the fact that Carla is pregnant, until she tells him that he can no longer do things that she can't while she is pregnant.
J.D. challenges a urologist's assessment on a consultation for a patient in need of a risky surgical procedure. He also starts to fall for her.
J.D. plans a date with Dr. Kim Briggs on their night off, but Elliot gets in their way.