In quaint Everwood, Andy has a secret that could ruin his relationship with Ephram. Meanwhile, Ephram is happily dating Amy, but overwhelmed by college preparations. Andy shares his office with another doctor (Scott Wolf) and becomes close with a married woman (Anne Heche). And Ephram and Amy befriend a new girl (Sarah Drew) in town. James Earl Jones, Elizabeth Mitchell and Chris Penn guest star.
Dr. Andrew "Andy" Brown, a world-renowned neurosurgeon who came to Everwood, Colorado, to start over and become a better father, is raising his two kids, preteen Delia and teenage Ephram, by himself.
At her father's suggestion, a heartbroken Amy is determined to make the most of her senior year in the wake of Ephram returning from New York and telling her that piano has to be his number one priority.
Ephram regrets promising Nina that he would watch over Hannah at school, especially when Hannah's constant presence interferes with his time alone with Amy.
Andy is uncertain about what to do when Delia naively stumbles upon Nina's sex toy and starts asking questions.
Dr. Brown is embarrassed after he picks a fight with Everwood's "patron saint," Amanda Hayes, who, unbeknown to Dr. Brown, has been caring for her profoundly disabled husband for the past five years.
Dr. Brown worries that Ephram is beginning to question himself and his chances of getting into Juilliard after he applies to a college in Colorado as a backup plan.
When Jake secretly informs Dr. Brown that Ephram came to him for an STD (sexually transmitted disease) test, Dr. Brown and Dr. Abbott decide the best plan of action is to convince Ephram and Amy to abstain from sex.
Struggling to select the music program for his Juilliard audition tape, Ephram seeks guidance from his music teacher and mentor, Will Cleveland, but Ephram faces losing one of the most important relationships in his life after he hurts Will's feelings.
Ephram and Amy decide they're ready for sexual intimacy in their relationship and make romantic plans to meet at the Abbotts' cabin, but the enormity of the situation proves too much for the couple to handle.
Realizing that his feelings for Amanda are only growing stronger, despite his best efforts to maintain a platonic friendship, Dr. Brown decides it is best to refer her husband's case to Dr. Abbott.
Following Amanda's decision to send her husband to a world-renowned treatment facility, Dr. Brown is rushed to the hospital after he collapses in front of Dr. Abbott as a result of the stress and guilt he has been feeling over his affair with Amanda.
When Jake's girlfriend from Los Angeles arrives in Everwood unexpectedly, Nina comes to his rescue with a sympathetic shoulder to lean on--and the possibility of more.
Dr. Brown faces the repercussions of his affair with Amanda when Nina accidentally discovers them together and questions Dr. Brown's integrity.
Dr. Brown and Amanda decide that it's time to tell Delia and her friend Charlie about their relationship before they hear about it elsewhere, but Charlie's emotional reaction makes them question what they're doing.
Just as they've become somewhat comfortable with their new relationship, Dr. Brown and Amanda receive word that Amanda's husband, John, has experienced a miraculous breakthrough in his recovery.
Feeling conflicted over the recent news about Madison and not willing to jeopardize Ephram's Juilliard audition, an angst-filled Amy tells Ephram that he should take his father to New York instead of her.
On the morning of his Juilliard audition in New York, Ephram meets Madison (recurring guest star Sarah Lancaster) for coffee and becomes distraught when she tells him that she was pregnant with their child.
After returning from New York feeling lost and confused and needing Amy for support, Ephram considers his options in the wake of his ex-girlfriend's life-altering revelation.
When Jake's younger brother comes to visit and confides that he doesn't see a future for Jake and Nina, Jake seeks counsel from an unlikely source--Dr. Brown.
To Dr. Brown's dismay, Ephram makes a bold move in an attempt to raise money for a plane ticket to Europe.
Feeling there is nothing to keep him in Everwood and desperately needing distance from his father, Ephram prepares to leave his family and friends for a new life in Europe.
In the season finale, Dr. Brown discusses with Delia the possibility of leaving Everwood to accept a prestigious position with a Chicago hospital. Uncharacteristically upset over this news, Dr. Abbott gives Dr. Brown a reason to stay.