The new chief of medicine turns out to be as callous as Dr. Kelso, J.D. gives up on his intern class after they let him down, and Eliot is too self-absorbed to realize that Keith is still hurt from their breakup.
J.D. and Elliot begin contemplating whether they're back together, or whether they even want to consider going down that road. Meanwhile, Dr. Cox's mistrust of surgeons reaches the tipping point for Turk.
J.D., Elliot, and Dr. Cox all choose the intern that they will take under their wing for the year, only to be sorely disappointed by each of their choices.
Dr. Cox is up for the Chief of Medicine position, but he's not sure if he wants it. Meanwhile, J.D. confronts his intern about her callousness toward patients, and Elliot asks for Turk's help in her love life with J.D..
Dr. Cox has trouble adjusting to his new job as Chief of Medicine, and Carla gets in trouble with the other nurses because of her relationship with the doctors.
Elliot misses J.D. while he is away. Turk announces that he and Carla are having a second baby, but nobody seems to care. Dr. Cox begins to wonder if Carla's attitude toward her job and her patients has changed.
J.D. and Turk direct the intern comedy show, but are mortified to discover that the biggest joke of the night is at their expense. Meanwhile, Elliot tries to get Denise to hang out with the other interns.
Turk is inspired to perform an experimental procedure on a paralyzed teen by a story on SportsCenter, Jordan is mad that Perry is wearing a wedding band, and the janitor thinks his new relationship is in trouble.
Everybody goes to the Bahamas to surprise the Janitor and Lady and attend their wedding. While there, J.D., Turk, and Dr. Cox come to the realization that their relationships are in trouble.
JD and Elliot are disturbed when Kim and Sean begin dating, and JD's son appears to like Sean more than him. Meanwhile, Dr. Cox has reservations about promoting Turk to Chief of Surgery, and Kelso admits himself into the hospital.
J.D. is mad at Turk when he overrules him on a medical decision in his new role as chief surgeon. But did he do it just because J.D. is moving away to be close to his son and taking a new job at another hospital?
The doctors reunite to teach med school to a new set of students, but J.D. is not sure after his first day whether he can make a difference and connect with any of his students.
Lucy ignores Dr. Cox's advice not to get emotionally invested in her patients, and learns her lesson the hard way. Meanwhile, Denise is hurt when she becomes emotionally involved with an intern who is only in it for the sex.
When Drew lets Dr. Cox down, he is then forced to turn to JD for help. Meanwhile, Lucy asks Dr. Mahoney to be her mentor, but she is too preoccupied with her own issues as a doctor to help.
JD spends his final day as a teacher trying to find out who gave him a negative review, Lucy looks for a "blood buddy," and Dr. Cox tries to convince Denise that Drew has taken charge of their relationship.
