There's no Chief of Medicine at Sacred Heart and the place is falling apart. There's no one to say, keep the Janitor from scrubbing in on Turk's surgeries or to just stop people from looting.
As much as he couldn't stand Dr. Kelso, Dr. Cox realizes somebody's got to keep things running at the hospital. He gets a call from the Board offering him the Chief gig. Jordan's excited about being rich enough to afford a second nanny who can listen to the first nanny's boring responses. But after talking to Kelso about how tough the job is, Cox isn't sure he wants it.
J.D. comes home to find Elliot baking cookies. She just baked a big batch and has prepared for her one-and-a-half cookies per day schedule by donning her comfy, stretchy "cookie pants." We're all wondering where we can get pants like that because we love cookies!
J.D. wolfs down his entire dozen knowing that, with Carla out of town, Turk's sweet tooth is going to be unstoppable. Elliot doesn't believe that Turk would go to such extraordinary lengths just to get some cookies, but she's sorely mistaken. The next morning, J.D. heads off to work, but before he does, Elliot suggests that they have sex that night, the first time since they started dating again. J.D. is obviously excited.
Later that morning, J.D. checks in on one of his favorite patients, an older man with heart disease. J.D.'s intern, Jo (really it's Denise), suggests they order a painful and invasive procedure as a test. J.D. shuts her down, thinking she's just being unfeeling as usual. But Jo orders the test anyway and, just as J.D. is about to unload on her, the results confirm that the man has stomach cancer. J.D. apologizes and says he's not going to ride her so hard anymore, at which point Jo snaps at him and storms off. Anyone else caught off guard by that?
Elliot's having a bit of a meltdown. She's built up this idea of being intimate with J.D. again and she desperately wants it to be perfect. She shows up at Sacred Heart, still in her cookie pants, to ask Turk to help her come up with J.D.'s ultimate sexual experience. Yeah, asking a guy's best guy friend how to plan an ultimate sex session is probably not the best plan, but Turk knows a surprising/disturbing number of things that will and won't work for J.D.
Elliot demands to know what makes things so great between Turk and Carla. He explains that what makes it special is that they don't have to try so hard. They can set aside the childish, neurotic stuff and just be together. Think J.D. and Elliot can do that?
Kelso tells Cox that what he said before was all true, but he had to prepare him for what to expect. Bob admits that he was the one who recommended him to the Board and that he is the man for the job. Cox takes the position and, despite their best efforts to keep hating each other, they're starting to actually become friends...slowly. We'll see about that.
J.D. confronts Jo to find out why she's so upset and she admits that she likes being pushed. She doesn't want him to just give up on her. She loves the "nuts and bolts" of medicine, but caring about patients is a real challenge for her, but she still wants to be challenged. J.D. agrees to keep pushing her, but lets her know that he can't fix her—she's going to have to work on her own hang-ups, he's got enough of his own. True enough.
J.D. comes home to find Elliot sitting on the bed, still in her cookie pants and he tells her that she looks beautiful. Awww.