As Turk and Carla return from their honeymoon, J.D. prepares for his first day as a qualified doctor. Elliot is still infuriated with him over their break-up. The hospital has a new psychiatrist, the somewhat dippy Dr Molly Clock. Dr Cox warns J.D. he still has much to learn.
Elliot, who thinks of Molly as her mentor, finds out that she isn't perfect. Carla gets tired of Turk waking her up when he enters the bedroom and enforces a bedtime on him. J.D. loses what little respect of his residents he had.
J.D. makes-out with Molly at her going-away party. He then gets approval from Elliot to sleep with Molly before she moves away. Dr. Cox has to complete community service in an ambulance with a Paramedic who talks endlessly.
J.D. takes matters into his own hands, when searching for a relative for his favorite patient. Meanwhile, Elliot is fed-up with co-workers not taking her seriously, and discovers she can get her way by flaunting her femininity with some help from Carla and Jordan.
J.D. tries to pawn off Elliot as his 'sidekick' but is shocked to find that she figures out something before he does. Turk has a realization and tries to come to terms with his Diabetes. Meanwhile, The Janitor tries to impress Elliot by gathering up the 'Brain Trust' to upstage Ted's band.
While at a nightclub J.D. hits it off with the bartender who says she needs a doctor. She arrives at the hospital with her boyfriend who turns out to have gonorrhea. J.D. is bound by doctor patient confidentiality so can't tell his girlfriend.
JD's date with Kylie doesn't go as planned, and when JD makes a mention of SARS, a quarantine begins. Carla and others tell about their horrible first dates, and Turk finds out that Carla once dated Dr. Cox. Ted and Todd fight over Danni, who's back in town, and the Janitor makes a bet with Dr. Kelso that lands him in a large debt. Laverne's birthday is spoiled when everybody else in the quarantine wants to get some of her Face Cake, especially Kelso.
The discovery that his latest patient is a comedy writer tips J.D. into a sitcom fantasy, complete with the dreaded laugh track. Turk and Carla worry that the romance has left their marriage. Cox volunteers to trim $26,000 from the hospital budget to avoid Kelso firing a cafeteria worker.
Carla and Turk decide to ask J.D. to move out of the apartment, leaving J.D. temporarily homeless, but it isn't long before they start to miss having him around...thus resulting in them realizing something they hadn't expected. Dr. Cox's competitive high school friend Ron comes to visit, Dr. Cox discovers that his (Ron's) son is autistic.
J.D. intervenes when Carla and Turk have relationship problems, suggesting they go for a few drinks...yet J.D.'s friendly gesture only makes things worse when he and Carla share a drunken kiss. The Janitor blackmails Dr. Cox when Jordan is unaware of how he (Dr. Cox) is treating they're'e son. Meanwhile, Elliot deals with a patient with a strange (more than eyebrow raising) condition.
Turk claims that he does not desire attention like Cox. To prove him wrong, Cox takes the credit when Turk saves a man's life. Meanwhile, Elliot tries *not* to ruin her relationship, and it's a battle of wits between Kelso and the Janitor.
J.D. is moving out. Kelso hiring Jordan makes Cox go nuts. Elliot realizes there is something wrong with her relationship. She also applies to another hospital, which upsets Carla, because she doesn't want her to leave.