J.D. starts off as an attending physician and leads some interns through their first day. Elliott works on her fellowship at a different hospital, trying to stay off the grid, while Turk and Carla try to make a baby.
J.D. worries about the way he relates with his interns. Elliott tries to shake a bad nickname.
J.D. rushes to accomplish things he'd hoped to do before his 30th birthday and competes in a triathlon. Turk fights to get a surgical attending position at the hospital, sometimes literally. Elliott has a hard time getting Jake to open up to her.
J.D. searches for something nice to say about Dr. Kelso during his awards dinner introduction. Elliott is crushed by her job at the free clinic. J.D. is upset that everyone knows about a game called Jiggly Ball but him.
Cox gets an unwanted visit from his religious sister Paige for Jack's baptism. Cox makes a point of letting J.D. know that he's not invited. Carla and Turk work to have a baby. J.D. helps the Janitor move in an effort to improve their relations.
J.D. and Cox let a patient pick between the two of them and she picks J.D. She later switches to Cox after J.D. mistakenly believes she wants to die peacefully without intervention. Carla tries to get hospital workers to show up for the annual photo.
JD has to come in on an off day when an intern pages him and then can't escape. Turk tries to get a heart to ensure that he takes part in an operation. Elliott tries to keep up the appearance of being a endocrinology expert. Jordan entrusts care of Jack to Carla.
Kelso quizzes the staff to discern responsibility with regards to the death of a patient. Carla asks people around the hospital what they'd do if they won the one hundred million dollar jackpot. Elliott mistakenly makes out with a married man.
JD meets a new woman with a lot of potential and Elliott tries to help him avoid the mistakes he made previously. Cox refuses to kiss his son now that he's starting to resemble a little man. The Janitor and Ted try to form an air band to win a bar prize.
JD introduces Julie to all his friends. Carla feels bad when the Janitor refers to a new nurse as "Young Carla". JD gets weirded out when Julie doesn't laugh at his humor and instead only says that it is funny.
JD is annoyed by his best intern Keith which doesn't improve when Keith hooks up with Elliott. Cox is upset when he gets close to the Janitor and then the Janitor denies him so as to not look like he's fraternizing with doctors. Turk gets in trouble with Carla when he decides he doesn't want female-friendly equipment in the hospital gym.
The Janitor makes a connection with a bird that winds up in the hospital. Turk is upset that Elliott doesn't have his number in her cell phone. Turk and Elliott misplace a letter a man gives them in case he doesn't make it through surgery. JD makes friends with an intern he's nicknamed Cabbage, but he's the one who makes all the mistakes when JD decides to come down tough on his interns.
JD and Dr. Cox's favorite patient continues the slide into illness, prompting the two to experience the five stages of grief. Dr. Kelso bumps Ted with his car, which gives Ted some much-needed leverage. Meanwhile, Turk is roped into going out with Carla, Elliot and Elliot's new man.
JD and the rest of the staff begin to tire of Keith the intern's seemingly infallible abilities, but balk when they discover he's been seeing Elliot. Meanwhile, Carla and Turk frustratingly try to get pregnant, and Dr. Cox is handed the toughest assignment in the hospital by Dr. Kelso after becoming the focus of a big magazine profile gives him a swelled head.
JD is torn between shaving off his hair to cheer up a chemo patient and keeping it for a woman who has shown interest in him and is fond of it. Turk and Carla continue to try and get pregnant and decide to make their lives less hectic to maximize their chances. Meanwhile, Elliot gets herself into an awkward situation with Keith, while Carla tries to find the patient she literally let slip away.
When Turk learns of Carla's pregnancy before she does, JD suggests he and Turk secretly tell everyone and make it a group surprise for her, but Carla’s desire to tell people herself forces the two to ask everyone to pretend they don’t already know. Meanwhile, Dr. Cox goes through an elaborate scheme to enact revenge on Elliott, and JD dupes the janitor into ingesting a tracking device.
JD frees up time to hang out more with Turk, only Turk realizes it's cutting into his own personal time alone. Dr. Kelso takes some time off himself to mourn the loss of his dog. Meanwhile, Dr. Cox and Jordan both go out on a date together with Elliot, and the staff finds itself humbled by a courageous liver donor.
When J.D.'s brother Dan comes for a surprise visit, Elliott learns that J.D. has been telling Dan that she's still into him. As everyone reacts to the pregnancy in there own way, Carla and Turk begin to discuss baby names, and despite his promise to her, Turk can't keep quiet about their initial choices.
Turk is accusing Dr. Cox of not being cool, Elliott is trying to extract information from Keith about his peers and J.D. just wants his mom to be able to see life through his eyes. After putting together a new baby room with Carla and Turk, J.D. decides to strap a camera to his head in order to get footage for his mother, but when the janitor destroys it, J.D. is left with nothing.
When it's discovered that Todd’s been lying about all his sexual conquests, Carla and Elliot suspect him of being gay. J.D is determined to have lunch with Mr. Cox, but when he finally gets the opportunity a former problem patient wants to teach him a lesson in responsibility.
After a decision results in the death of three of his patients, Dr. Cox shirks his duties and turns to drinking. Shocked, the staff does their best to cover for him at the hospital while each takes a turn trying to convince him how inspiring he is.
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 that he can do a lot of stuff but she can't since she is now pregnant.
J.D. challenges a urologist's assessment on a consult for a patient in need of a risky surgical procedure. He also starts to fall for her. Elliot considers breaking up with Keith for being too weak and Dr. Cox picking on him does not help his case.
J.D. plans a date with Dr. Kim Briggs on their night off, but Elliot gets in their way. Perry and Jordan celebrate Jack's milestone. The hospital pick a name for Turk and Carla's baby while somebody else is eagerly awaiting the results of a pregnancy test.