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S6E1 22분J.D. addresses the news that he is going to be a father and Dr. Cox is worried about how his anger is going to impact his offspring. Meanwhile, Carla and Turk prepare for the impending arrival of their new baby. Elliot feels left out because she is childless, while the Janitor wonders if he has wasted his life.
S6E2 22분J.D. and Kim start contemplating about their future and their baby's future. Meanwhile, Turk rushes Carla to the hospital after she goes into labor. And Jordan accuses Dr. Cox of not being a more defensive father towards Jack.
S6E3 22분J.D. and Kim are surprised of how much they have in common. Recently giving birth, Carla doesn't want to return to work. Meanwhile, Elliot tries to persuade Dr. Turner, a surgeon with thirty years of experience, that medicine is the better option to work with and that surgery could kill him.
S6E4 24분Dr. Cox feels like the TV character House when he has to solve several mysteries, one of them being Elliot's anger towards Dr. Kelso, while for some reason she is taking it out on Turk. J.D. tries to be a better boyfriend to Kim.
S6E5 24분Elliot begins enjoying luxuries since she has extra money with her new private practice gig. But eventually, J.D. becomes jealous of her and that forbids him the use of these privileges. Dr. Cox and the Janitor become roommates in one of the hospital suites, while Turk tries to convince Carla that she has postpartum depression and that she needs help.
S6E6 24분A new patient at the hospital wakes up and sees everything happening around her as a musical. Carla can't decide whether or not to return to work and Elliot must find a way to tell J.D. he can't move into her new house with her.
S6E7 24분The hospital is seen through the eyes of Dr. Kelso, who befriends an Iraq War veteran. The soldier's stay sparks a political debate among staff members.
S6E8 24분After being convinced to go to Tacoma for Kim's first ultrasound, J.D., along with Carla, Elliot, Janitor, Keith and Ted, takes Kelso's new RV on a road trip. Meanwhile, Jordan and Dr. Cox have trouble when Jordan's ultrasound reveals that the baby will need surgery.
S6E9 24분A Croatian Doctor comes to Sacred Heart, only to find out that he has to redo his Internship there. J.D. shows symptoms of 'Vasovagal Syncope', a condition that causes fainting and blackouts. Turk and Elliot argue over whose turn it is to take care of him, whilst Carla tries out her new excuse "I have a baby" and the Janitor takes a vacation.
S6E10 24분J.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.