When Dan resurfaces, J.D. is shocked to learn that his father has passed away. The reactions from his co-workers help J.D. a little, but the one person who he wanted to be there for him, Dr. Cox, is too busy with J.D.'s patients. Meanw...

Elliot becomes unsure, if she wants Molly as her mentor, when she finds out that Molly does not have a perfect home life. J.D. is tested in leadership skills when Dr. Cox yells at him in front of his interns. Carla and Turk try to come to a...

J.D. is shocked to hear Dr. Cox tell his interns that eventually, they will screw up and kill a patient. J.D. fears his first time killing someone will soon be upon him. Elliot is upset with Molly, after she disagrees about a patient's...

Dr. Cox is having issues with Jordan, since Ted revealed that they are still technically married due to some filing problems. J.D. has problems of his own as he can't shake off the tag of Co-Chief Resident the Janitor assigned to him, ...

Molly tries to reconcile J.D. and Elliot, while waiting to see which one Dr. Cox will give the Chief Resident position to. Molly and Carla are experiencing some subtle conflict and Elliot and J.D. begin to come together after long boughts o...

The new Dr. Molly Clock arrives with her spaced out personality and doesn't cease to call J.D. "Johnny". But J.D. is fine with it, because there is nothing that is going to bring down his last week of being a resident before ...

The big day for Turk and Carla has finally arrived, but a patient holds up Turk. With Elliot still angry at him, J.D. attempts to reconcile her with Sean as a way to make everything right again in their friendship.

J.D. is unsure what to do, when he realizes he made a mistake telling Elliot he loved her. The Janitor squares off against Dr. Cox after he loses the election of the janitors to Randall. Carla's brother Marc constantly puts Turk in a t...

Elliot asks Sean to move in with her, which only adds to J.D.'s problems. Turk is unsure why Dr. Miller's attitude towards him has changed, until he finds out that Carla un-invited her from their wedding. Dr. Kelso outrages Dr. Co...

J.D. hooks up with Danni again, after Sean returns, but he can't forget about his passionate night with Elliot. Meanwhile, Dr. Cox realizes, that he might actually have a crush on the one doctor he loathes.

Turk has to confront a young patient of his, when he accidentally cuts a nerve and the boy (who happens to be a concert pianist) loses use of one of his hands. Meanwhile, one of Elliot's patients unintentionally teaches her a lesson ab...

J.D. must keep a secret when Carla's "what-if" guy asks her out on a date. Meanwhile, on the other side of the argument, Carla hounds Turk for checking out other women. Elliot is also on the spot as Dr. Cox and Dr. Kelso both...

An ever present butterfly prompts the question on what could have happened different as Turk looks for his lucky do-rag for surgery, and Elliot tries to find a lost stuffed animal for a child needing a bone marrow transplant.

Jordan's friends Allison and Maddie come to town to provide moral support for Jordan after her brother's death ñ however, their constant presence does not provide any relief to Dr. Cox. Meanwhile, Turk tries...

Jordan's brother and sister return, but Dr. Cox learns that his brother-in-law Ben hasn't visited a doctor about his cancer in the two years he has been gone traveling the world.

Elliot finds herself perplexed over a simple procedure that leaves her questioning her career path. She goes to seek Dr. Kevin Casey's advice but becomes frustrated when she learns that the epiphany toilet, which the Janitor secretly i...