Season 3

A run-in with her old flame Sean and an accident in her new car lead Elliot to the realization that nothing good has happened to her in the three years that she has been at Sacred Heart. This realization drives her to take drastic measures, including a complete makeover, both inside and out, in an attempt to change her luck. Meanwhile, J.D. gets stuck with a patient, whose diagnosis he can't quite pin down, and when Dr. Cox denies him any assistance, he looks to Carla and Turk to help him out. While Dr. Cox is busy not helping J.D., he takes the time to make amends with Dr. Kelso.

J.D. is feeling left out of his friendship with Turk and gets hurt when Turk is scared of opening up to him. Meanwhile, Carla is driven crazy over an unidentified urine sample, and Elliot tries to balance Sean and her career, so that one doesn't end up getting in the way of the other.

Finding difficulties training his interns, J.D. asks to Elliot for some help. She tells J.D. about Sean, who gave Elliot great tips based on his dolphin training that fit perfectly for her interns. Dr. Cox finds the ideal pediatrician for his son: Dr. Norris, who acts and looks just like him. However, Dr. Cox is quick to find a problem with him once Jack develops a cough that scares both him and Jordan.

Sean is a bit surprised and disturbed to learn about Elliot and J.D.'s history together, but it turns out his anger is really a cover up for his upcoming six month long trip and he doesn't want Elliot to explode. Dr. Cox. is forced to swallow his pride and actually ask for help when he decides to throw his hat in the ring for the Residency Director position at the hospital. Carla picks up an extra shift as a surgical nurse, which allows her to spend the day working alongside with Turk, to his great annoyance.

Dan decides to stay with J.D. for a while after their mom's new fiancé kicks him out, but after spending some quality time with him at the hospital, Dan isn't sure if he likes the cynical person his little brother has become. Elliot tries to deal with her own problems of a long distance relationship and decides to try moonlighting as a pet examiner with Carla to save up money.

A chance meeting in the elevator sparks a new friendship between J.D. and the mysterious Danni whose ongoing dialogue about her ex forces J.D. to talk about his feelings for Elliot. Carla's brother Marco comes to visit, but he still hasn't forgiven Turk for mistaking him for a valet at their mother's funeral. Unfortunately, Turk can't even apologize because Marco can't speak anything but Spanish. At the hospital, Dr. Cox relishes his new job promotion but is surprised when J.D. doesn't follow his lead in contradicting Dr. Kelso's orders.

As J.D.'s relationship with Danni progresses, he and Dr. Cox are forced to spend more time together outside of the hospital, to Perry's great chagrin. Meanwhile, as they each deal with problems in their own relationships, Carla and Elliot work to find their own balance between their personal and professional relationships. Dr. Kelso accidentally punctures his eardrums giving the hospital staff an opportunity to tell him how they truly feel about him.

Elliot struggles to find her defining moment after Turk performs his first solo surgery. Dr. Cox deals with the reality of growing older when his back goes out. J.D. finds out that many of the hospital staff don't know the Janitor as he does.

Elliot feels uneasy with the proper terms for sexual organs, especially after performing a pelvic exam; J.D.'s patient refuses to have surgery for prostate cancer.

Carla and Elliot try to help a patient, Maggie, lose her virginity as she prepares to die. Walking in on her sister and Dr. Cox prompts Danni to move in with J.D. Dr. Cox attempts to convince Turk to do a kidney transplant for a patient he has "moved up" the list. But a personal grudge seems to stand in the way and may decide whether the patient lives or dies.