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J.D. starts his residency, but has to start it coping with the relationship problems between him and all his friends after Jordan revealed a lot of secrets; Dr. Cox is furious at him for sleeping with his wife, and Elliot is embarrassed to be around him after it is revealed she still has feelings for him. However, over time, these problems resolve themselves and things continue as normal ("My Overkill"). But J.D. then has to cope with the new responsibility that comes with being a resident, as he, along with Elliot and Turk go a whole night shift in charge of the hospital. ("My Nightingale")
A few weeks later, J.D. is put into a tricky situation as he has to choose between Reno and Dr. Cox's respect when Dr. Kelso offers a trip to Reno for whoever presents the most interesting medical case-study, and even though J.D. finds a case more interesting than everyone else, he knows that Dr. Cox is actually proud of him for not playing along with Kelso's game. However, J.D. decides to present the case study after realizing that furthering his career is more important than Dr. Cox's respect, but in turn, Dr. Cox respects him for making that decision for the right reasons. ("My Case Study")
J.D. continues on with his job and friendships, including finally convincing Carla to open up her secrets, but accidentally reveals her secrets to other people, betraying her trust. ("My Big Mouth") In adjusting to his new position at the hospital, J.D., feeling more like a doctor, proudly dons a white lab coat and attempts to stand up to the Janitor and Dr. Cox. A new patient, Mr. Blair, has been admitted for a severe sinus infection and J.D. is treating him. As Mr. Blair's infection persists, J.D. decides to administer a stronger antibiotic intravenously. The patient ends up losing his sense of smell and blames J.D. After much anxiety, J.D. finds that it wasn't his fault after all and confronts Dr. Cox for seemingly placing the blame on him. ("My New Coat")
J.D. then has problems when his brother, Dan, comes to stay, as he realizes how little his brother has actually achieved in his life, and tries to hide this from everyone. However, eventually Elliot convinces J.D. to confront Dan about it, but Dan walks away. ("My Big Brother")
Julie Keaton, a pharmaceutical representative comes to Sacred Heart. When she flirts with J.D., Dr. Cox interrupts. After venting he storms off and takes J.D. with him. Moments later, Elliot asks J.D. for advice on a patient and tells her to "wait and see", but she signs her up for surgery after she gets the feeling that J.D. thinks he is a better doctor than she is. The patient dies and J.D. re-states that he was correct. J.D. tries to apologize but Elliot storms off. After Dr. Kelso told Elliot that all "wait and see" doctors would never be great doctors, J.D. thanked her for not rubbing it in his face, and Elliot makes a joke right to his face. In the cafeteria, J.D. admits that he really is not daring in his career or life, and Elliot drags him along to go bungee jumping. ("My First Step")
A few weeks later, J.D. has problems with his friendship with Turk after Turk finds him a job, but secretly keeps some of the money for himself. However, when Turk reveals he is considering asking Carla to marry him, they forget all about their problem and the two of them, along with Elliot and Carla, go out for dinner, despite being deeply in debt. ("My Fruit Cups")
At this stage of his life, J.D. feels as if he is doing great; especially after he corrects an incorrect diagnosis made by Dr. Cox, which J.D. learned about when he watched a medical special on TV. However, to prove to J.D. that it was simply luck that he watched the program and gave the correct diagnosis, Dr. Cox gives J.D. a patient with the same ailment as his own patient. When J.D.'s patient dies, despite the fact that he has done the exact same treatment as Dr. Cox did for his patient, he realizes that it was just down to luck that his patient died while the other did not, just the same as it was luck that he knew the diagnosis for the other patient. ("My Lucky Day")
Because Sacred Heart seems to be taking over all his personal life, he decides to fight this by asking Lisa, the gift-shop girl, out on a date, which she accepts. The date goes well, but when they go into kiss at the end, J.D.'s mind goes back to patients he has seen throughout the day with disgusting health problems - which puts him off and he pulls out of the kiss. When they try again, the kiss goes okay except J.D.'s "little J.D." has no response at all, as the disgusting thoughts have put him off. This just proves to J.D. even more that the hospital is taking over his personal life ("My Monster"). However, J.D. and Elliot realize they both still have feelings for each other, and they begin to have regular sex - and they decide to become "sex buddies". However, after Elliot's performance in work begins to worsen because of the sex, Elliot decides to stop being sex buddies and just be friends. ("My Sex Buddy")
J.D. helps a patient who's pregnant wife has an irregular heartbeat. He sits down with him and comforts him. Later, J.D. learns that one of his favorite patients, Elaine, is back and in need of a heart transplant. J.D. and Elaine discuss the balance of life, which annoys Dr. Cox. The episode concludes with Elaine dying, and a big musical scene with all the characters, playing out everyone's emotions lyrically. ("My Philosophy")
Dr. Townshend comes to Sacred Heart and J.D. is paired with him to work on a patient. He advises J.D. to do an "old school" procedure on a patient, even though it is dangerous. During this procedure, J.D. accidentally nicks the patient's carotid artery but Dr. Townshend says he will take the blame. J.D. walks into Dr. Kelso's office and tells him that he nicked the artery, but only because Dr. Townshend told him to do an outdated and dangerous procedure. Dr. Townshend admits that he does not attend the seminars about new medical procedures and Dr. Kelso is forced to fire him, even though he is his best friend. ("My Brother, My Keeper")
After being yelled at by Dr. Cox, J.D. shows up at his apartment and tells him he requested to be transferred to another attending physician. After his therapist helps him realize that J.D. can somehow get through to him, Cox asks for J.D. to switch back to him, and J.D. immediately agrees. ("His Story")
While golfing on the roof, J.D. takes a swing and he and Turk hear a car crash. They rush inside. Later, the two residents meet their patient Mr. Foster who was in a car accident after a golf ball flew through his windshield. The doctors freak out but do not tell him that it was them who caused his accident. They decide to never tell anyone. Dr. Cox asks J.D. to keep an eye on Jordan who is preparing to give birth. J.D. believes that karma is affecting their lives, so they admit to Mr. Foster that they were playing golf on Sacred Heart's roof. Mr. Foster tells them that his accident happened downtown, so it was not possible that they caused it. J.D. realized that their karma may have been because of other patients. He entered Jordan's room to keep her company and she confessed her true feelings of Dr. Cox and confides in J.D. that Perry is Jack's father. ("My Karma")
J.D. becomes friends with Dr. Peter Fisher, a private practice doctor who tells J.D. secrets about Dr. Cox. Perry tells J.D. that Dr. Fisher is a bad person, but J.D. seems to like him and continues to help him treat a patient. Eventually, during an argument between Peter and Cox in the break room, it is revealed that Jordan cheated on Dr. Cox with Dr. Fisher, which led to their divorce. J.D. chooses Dr. Cox. During all of this, J.D. tries to tell Dr. Cox that he is the father of Jordan's baby, but can't because the only time he can tell him is when they meet in the toilet, which is when they are always interrupted by her. ("My Own Private Practice Guy")
Jamie Moyer the T.C.W. is back visiting her comatose husband Jack Moyer and she chats with J.D.. When no one will grab beers with him, Jamie overhears and asks to go out with him as his wingman. The next day she appears at his apartment and tells him that she is ready to move on with her life and asks him to ask her to dinner sometime. Back at Sacred Heart, everyone comments that he is a terrible person, but he lashes out at them for complaining about their relationships when he is lonely and only wants companionship. He takes Jamie up on the offer and the two go for dinner, but does not go back to her place with her because he doesn't want her to move too quickly. He spends the rest of his night pondering his singleness at Sacred Heart. ("My T.C.W.")
J.D. begins his surgical elective. At the hospital he doesn't quite fit in with the jock-like surgeons and ends up being treated to a hanging wedgie. At lunch, J.D. mocks Turk for participating in ballet in college. Turk is upset that J.D. would sell him out so easily. At the bar, Turk tells J.D. that he has always been his friend because he has never been afraid to be himself. J.D. takes this to heart and sits with the nerds the next day at lunch and gives himself the nickname "King of the Nerds" ("My Kingdom").
Jack Moyer dies, and J.D. goes to see Jamie at the funeral. They end up having sex, but J.D. is worried that Jamie is not ready for another relationship yet. Back at the hospital, J.D.struggles to communicate with a German patient. Elliot turns out to be fluent in German and finds out that the patient's brother had withheld the information from the German patient. When the patient's test results get back and it's apparent that he will be fine, J.D. contemplates on whether it's worth telling him at all. He eventually decides in favor of it, using Elliot as the translator. In the process, J.D. realizes that just as the patient's brother tried to protect him when he shouldn't have, so was J.D. being overprotective of Jamie and her decision to pursue a relationship with him. Armed with the knowledge, he meets her and tells her that he realizes her husband is gone for good and that if she feels ready, he'll take her...in front of her late husband's parents ("My Interpretation").
However, once Jamie's husband dies, the taboo has gone and Jamie is less interested in J.D. - and Elliot suggest that it may be because Jamie is a "drama queen" who only enjoys the relationship if dramatic events are occurring. At first, J.D. acts dramatic to keep the relationship going smoothly, but quickly grows tired of this and tells Jamie that he only wants a relationship if she does not base it on drama. ("My Drama Queen")
When J.D. and Turk's old childhood friend, Spence, comes to visit, it makes J.D. think about whether he enjoys his job or not, and decides to spend his time on-call in a hot-tub with Spence and Turk. However, this gets them in trouble when they arrive at the hospital drunk, and Dr. Cox sends them home. This makes J.D. realize the reason he originally got into medicine; to help people, even if it makes things worse for them - and J.D. realizes he does enjoy his job, even if it can be hard. ("My Dream Job")
|J.D. Character History: Season One • Two • Three • Four • Five • Six • Seven • Eight • Nine|