The main storyline of this episode was Dr. Cox being offered the Chief of Medicine position. Kelso warns Cox about what taking the position will do to him and he quickly decides not to. Jordan gets extremely pissed at Kelso for talking him out of it and for Cox not taking the position. After Kelso calls Cox scared for not taking it, Cox steps up and takes the position and Kelso admits he's the one who recommended him for the position. They're becoming friends and we have a new Chief of Medicine!
The episode opens with Elliot making cookies for J.D., who quickly consumes his fearing Turk will steal them (Carla is out of town and this is the only time he can steal sweets). Turk does eventually sneak in during the middle of the night and takes them. In the morning, Elliot promises J.D. when he gets home that night they're rekindling things sexually and he's going to get "wild sex." Elliot then comes in to work on her day off to annoy Turk on what she needs to do to give J.D. the best sex (and he owes her cause of the cookies!). Turk eventually just tells her to be herself.
J.D. and Denise's patient is having stomach pains and Denise wants to order an endoscopy but J.D. won't let her because it's uncomfortable for the patient and he thinks it's just hurtburn. J.D. yells at Denise for still being insensitive and she orders the test behind his back. When the test comes back positive, J.D. goes to apologize to Denise and she yells at him. Denise wants J.D. to keep pushing to make her a better doctor. She's growing on us.