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Dr. Cox is named the best Doctor in the area by a big publication; After struggling to conceive, Carla blames Turk's fertility; Elliot finds out J.D. dislikes Keith.
Dr. Cox's born-again Christian of a sister, Paige (Cheryl Hines) visits the hospital to ask him to be in her son's baptism; Elliot tries to convince Turk that babymaking is romantic.
J.D. and Turk finds out Carla is pregnant before she does. J.D. convinces Turk to tell everyone in the hospital to surprise Carla.
After five years of working at Sacred Heart, J.D. gets the funny feeling the same events keep occurring. Meanwhile, Cox returns to work but loses his self-confidence.
J.D. and Kim's romance escalates, but Elliot, who recently became friends with Kim, won't give them time alone. Dr. Cox and Jordan celebrate Jack becoming potty trained.
Feeling guilty over the death of three patients, Dr. Cox comes to work drunk and is forced on a league of absence. The whole staff except J.D. takes rotations visiting Cox.
J.D. falls for Dr. Kim (Elizabeth Banks) after she removes her wedding ring and instantly appears; Elliot considers breaking up with Keith when he refuses to stand up for himself.
Carla is forced to do Kelso's normal job of rejecting people's requests; J.D.'s patient who gets a liver transplant recovers while his brother who donated gets worse.
J.D., Elliot, Turk and Carla are all under investigation after the death of a patient. It's found that all four were doing irrelevant things.
J.D. finds himself lying to protect his visiting brother Dan's feelings; Carla and Turk can't decides on a baby name; Cox is forced to work with Ted.
J.D. tries to get rid of Keith while favoring a different intern, "Cabbage." Meanwhile, the office says good to Mrs. Wilk while the Janitor keeps a magpie who likes to steal things at the hospital.
J.D. gets called into work on his day off and all he wants to do is go home; Elliot tries to convince everyone she's an endocrinologist after her short-lived fellowship.
J.D. ends up being mean to his interns after he finds out they only laugh at his jokes out of fear; the hospital staff tries to avoid Jordan to get her to go away; Elliot's fellowship ends abruptly.
In an episode narrated by the Janitor, J.D. tries to make a video postcard for his mother, but gets locked in the water tower by the Janitor while the Janitor bonds with a quadriplegic patient.
After repeatedly running into and blowing off an annoying patient, Jill (Nicole Sullivan), J.D. feels guilty when she commits suicide via a drug overdose and he never saw the signs coming.
As the hospital says goodbye to a dying Mrs. Wilk, Cox and J.D. go through the five stages of grief. Meanwhile, Elliot realizes her booty call with Keith has become a relationship.
In an episode narrated by Carla, she gets a fertility test when the new nurse makes her feel old. Meanwhile, J.D. gets bothered by the little things with Julie.
J.D. confuses a patient's reaction to her approaching death as a desire to end treatment; Carla tries to gather the hospital staff for a group photo.
J.D. encourages his patients to go the extra mile with their patients; Turk and Carla finds out they're having problems conceiving because of their stress.
Now an attending, J.D. has to deal with his own set of interns. Meanwhile, Turk hesitates at the though of Carla getting pregnant while Elliot starts her fellowship at County Hospital.
J.D. struggles to find something nice to say about Kelso during his introduction at an awards dinner; Carla and Turk try to help Elliot get her job back.
J.D. and Elliot agreed to each find respective booty calls; Meanwhile, Carla encourages Turk to fight for a female-friendly gym and the Janitor and Cox forge a friendship over beers.
J.D. goes on a blind date with a patient's niece and takes Elliot's advice; Turk joins the hospital air band; Cox worries about being a bad father.