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After Jordan revealed that she slept with J.D., he expects the worst from Dr. Cox. Elliot, embarrassed by Jordan's revelation about her lingering feelings for J.D., is avoiding J.D. at all costs. Carla is angry with Turk for not telling her that Dr. Cox was in love with her, and Dr. Cox is annoyed at Dr. Kelso for being played for a non-existent promotion and at J.D. for sleeping with Jordan. Guest-stars Colin Hay as the troubadour. A new design for the opening credits was introduced with this episode, with Neil Flynn (the 'Janitor') listed as a regular cast member. The episode's title is derived from the featured song 'Overkill', which Colin Hay performs onscreen.

The residents spend a night on-call with no attending physicians available and deal with the responsibility of running the hospital on their own and having to make a tough decision about a patient. Meanwhile, Cox struggles with his feelings for Jordan.

Dr. Kelso starts an impromptu competition with the residents, offering an all-expenses-paid medical conference outing in Reno if they can bring him the most interesting case study. J.D. wants to compete, but fears he will fall out of favor with Dr. Cox if he does. The entire hospital takes advantage of Dr. Kelso's annual good mood the day after he renews 'marital activities' with his wife Enid. Elliot worries that she isn't getting along well with Carla. Guest-stars Michael McDonald as Mike Davis.

J.D. and Carla's relationship deteriorates when J.D. accidentally reveals some of Carla's secrets. The surgical residents compete for a trip to Mexico with Dr. Kelso. Elliot worries that she isn't presenting a competent image to Dr. Cox and takes on some harrowing cases to improve it.

J.D. gets an ego boost by wearing a white doctor's coat, but also has to accept the increased responsibilities that come with it. Elliot's reputation suffers when she has a one-night stands with another Sacred Heart doctor.

J.D.'s older brother Dan (Tom Cavanagh) drops by for a visit, but J.D. can't hide how ashamed he is of his brother's life. Turk learns a lesson when he makes a bet with Dr. Cox on whether a patient lives or dies. Meanwhile, Sacred Heart staff is in costume for Halloween, and one person in particular is wreaking havoc in a gorilla suit, much to Dr. Kelso's disgust.

Julie Keaton (Heather Locklear), the attractive pharmaceutical representative on whom everyone has a secret crush, arrives at Sacred Heart, and tensions between her and Dr. Cox run high. J.D. and Elliot bicker over which one is the better doctor. Carla considers the drawbacks of being 'just a nurse'.

Dr. Cox and Julie (Heather Locklear) hook up, but Cox's new happiness is complicated when a pregnant Jordan arrives. J.D. and Turk suffer from a poor financial situation, and continue to steal food and toilet paper from the hospital. Elliot's father cuts her off after she refuses to become an OBGYN as he wishes.

Elliot is forced to move out and also has to deal with a malpractice suit. J.D. shows up Dr. Cox and an unofficial competition begins between them. Guest-stars Alan Ruck as Mr. Bragin, and features cameo appearances by David Copperfield and John Ritter. This is the only episode in which the Janitor does not appear.

Problems develop in the relationships of Turk and Carla and of Dr. Cox and Jordan. J.D. considers exactly how much the hospital consumes their lives; the stress and general gross experiences he deals with everyday are stealing his 'mojo' just as he starts dating Lisa the gift Shop Girl (Sarah Lancaster). Having lost the apartment her father paid for, Elliot is forced to live in the back of a moving truck as she has no time to find another place, and J.D. loses his mojo while dating Lisa the gift-shop girl.

Not wanting to repeat their last disastrous relationship, J.D. and Elliot agree to remain 'sex buddies,' but J.D. isn't satisfied with this arrangement. Turk tries to help out Elliot with her workload, but his efforts backfire. Carla learns a lesson about why hospitals can't always give definite answers.

J.D.'s feelings for Elliot continue to grow even after they break off casual sex; he tries seeing Lisa (Sarah Lancaster) again. Dr. Cox and Carla misdiagnose a hypochondriac (Richard Kind) patient after not taking his claims seriously. Dr. Kelso teaches Turk a lesson about the small lies their patients tell them.

Elliot demands single-sex locker rooms from Dr. Kelso, who is considering ways he might acquire a bigger office. Turk pops the question to Carla, but not in the way he'd originally planned. One of J.D.'s favorite patients (Jill Tracy) is back in the hospital for her heart condition.

Turk's brother Kevin (D.L. Hughley) comes to visit with important news; Turk's feelings of inadequacy and debt to his brother surface. Dr. Townshend (Dick van Dyke), an elderly doctor liked by everyone, runs into trouble with his best friend Dr. Kelso when J.D. screws up an out-dated procedure under his supervision.

This episode is narrated from Dr. Cox's, rather than J.D.'s, viewpoint. Dr. Cox discusses the hospital and Jordan in his sessions with his psychiatrist, Dr. Gross (Eric Bogosian). Elliot is thrilled to meet Paul Flowers (Ricky Schroeder), an attractive and charming doctor...until she learns he's actually a nurse. Carla finally says yes to Turk's proposal.

J.D. and Turk attempt to cover up the fact they were hitting golf balls off the roof and may have caused the accident that landed their patient in the hospital, but the Janitor knows... Jordan finally gives birth, and reveals to J.D. who the father of her baby is, and asks him to keep her secret.

J.D. comes to admire his patient's private practice doctor, Dr. Peter Fisher (Jay Mohr), but is shocked to find out Peter was actually the reason Jordan and Dr. Cox divorced. The Janitor starts flirting with Elliot, and Carla begins to worry about her appearance. Features a cameo appearance by Jay Leno.

Dr. Cox switches from female to dog names for J.D. after an interesting bestiality rumor about J.D. makes the rounds. Dr. Cox competes with baby Jack for Jordan's attention; relationship troubles crop up for Elliot and Paul and for Turk and Carla. When J.D. accepts a date from Jamie Moyer (Amy Smart), the very attractive wife of a comatose patient, his friends give him flak for it. The title is an abbreviation for 'Tasty Coma Wife,' the moniker J.D. and Turk give to Jamie.

When J.D. does a temporary surgery elective, his friendship with Turk suffers as he tries to win popularity. The Janitor gets a new power saw. Dr. Cox's plays a prank on Dr. Kelso while he's away, and it gets a little out of hand. Elliot's slip of the tongue drastically changes her relationship with Paul.

J.D. attends the funeral of Jamie's (Amy Smart) husband, with predictable results. Turk has a sex dream about Elliot and is bewildered and embarrassed by it. Dr. Cox experiences still more mixed feelings about raising a child he still believes is not his.

J.D.'s relationship with Jamie (Amy Smart) takes a few interesting twists; Elliot correctly identifies her as a drama queen. Carla's mother dies. Dr. Cox is stuck with Ted in teaching a sensitivity seminar after Dr. Kelso witnesses Dr. Cox being particularly vicious towards a patient.

The end of the second year has the residents finding their jobs too monotonous; luckily, Spence (Ryan Reynolds), an old college buddy of J.D. and Turk's, visits and lightens things up, perhaps a little too much. Dr. Cox learns the truth about baby Jack and confides in J.D. he doesn't think he'd make a good father. J.D. encourages Cox to imagine being a father, and as Dr. Kelso further attempts to break Elliot's spirit, Dr. Cox steps in and punches him.