Dr. Brown and Dr. Abbott must put their striking differences aside to educate the town of Everwood after several of their teenaged patients are diagnosed with a sexually transmitted disease. To make sensitive matters worse, Dr. Abbott has reason to suspect that his son, Bright, may have been intimate with one of the patients. Meanwhile, Ephram pushes his romantic feelings aside to comfort Amy who is distraught over not being able to go to the Fall Dance with her boyfriend who remains in a coma.

Amy moves back home, but finds adjusting to her old life difficult, especially after her parents (Tom Amandes and Merrilyn Gann) discover she's taking birth control pills and her former friends give her the major cold shoulder. Elsewhere in Everwood, Ephram thinks Madison is going to break up with him and Andy testifies on behalf of Nina as she and her recently out-of-the-closet ex-husband (guest-star Dylan Walsh) battle for sole custody of their son.

Ephram and Amy decide to go to prom together as friends, but Amy can't get up the nerve to tell Ephram that she has feelings for him after they run into his ex-girlfriend Madison and Amy realizes that he's still nursing a broken heart. Meanwhile, Linda decides it may be time to leave Everwood behind, and Andy's mentor, Dr. Donald Douglas (guest star Philip Baker Hall), asks him to perform risky brain surgery on a patient who turns out to be Dr. Douglas himself.

When Amy accompanies Ephram to his Julliard audition in Boulder, a romantic moment leads her to confess her newfound feelings for him. Meanwhile, Andy struggles to convince his mentor Dr. Douglas (guest-star Philip Baker Hall) that he needs even riskier brain surgery than originally thought and that Andy is the man to do it. Dr. Abbott faces losing his medical practice after it appears no company will insure him. Lastly, Bright decides not to attend his graduation ceremony, much to the disappointment of his family.

Ephram regrets promising Nina that he would watch over Hannah at school, especially when her constant presence interferes with his time alone with Amy. Amy befriends Hannah out of a sense of charity, but soon finds Hannah so refreshing that a real friendship develops. Meanwhile, Andy tries to ignore the tension between Dr. Abbott and Edna, but his attitude forces Edna to quit and go to work for Dr. Hartman. Andy treats a 13-year-old patient (guest-star Carter Jenkins) whose mysterious injuries cause Andy to suspect the boy's mother (guest-star Elizabeth Mitchell) of abuse.

Jake's visiting accountant brother Brian (guest-star Tom Parker) from LA says he sees no future for Jake and Nina, prompting Jake to seek advice from Andy. Also, accepted at Princeton, Amy assumes that her father secretly sent in her application. Lastly, health issues create tension between Rose and Harold, but the tension turns to fear when Harold finds out that Rose has a 3-centimeter long tumor.