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.

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. 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.

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. 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. 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. develops a crush on a new physical therapist but due to his latest misfortunes, he finds it difficult to ask her out. Elliot asks Keith to move in with her, but is not willing to budge on her home rules. Turk breaks his arm and is sent back to residency by Dr. Kelso. Thanks to Dr. Cox, he realizes that he doesn't know as much about medicine as he thought.

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.