Amy and Ephram are able to see each other again after Ephram's summer in New York at the Julliard program. However, Amy begins to worry about their budding relationship when Ephram starts to act distant from her. Meanwhile, Andy feels guilty about not telling Ephram about Madison's situation; and Harold quickly befriends Everwood's newest doctor, Jake Hartman who's looking to start a practice in Everwood.

Amy sets out to make the most of her senior year even though she's still heart-broken that Ephram decided to put piano first over their relationship. Andy continues to debate whether or not to tell Ephram about Madison's pregnancy while Rose helps Bright decide what he wants to do with his life. Meanwhile, Jake's new marketing campaign for his practice starts to annoy Harold; and Nina asks Ephram to look out for a friend's teenage daughter, Hannah, who just moved in with her.

Ephram begins to regret agreeing to look out for Hannah when her presence gets in the way of him spending time alone with Amy. Soon Amy finds a connection with Hannah and the two become close friends. Meanwhile, Andy has a hard time ignoring the tension between Harold and Edna, especially when Edna quits and gets a job at Jake's practice instead while the case of a 13 year-old's suspicious injuries weighs heavy on his mind.

When Delia accidentally comes across Nina's vibrator, Andy isn't sure what to say or do when Delia asks him about it. Ephram struggles to write a love letter to Amy while Amy takes it upon herself to make Hannah popular. Meanwhile, Harold and Rose worry that Bright isn't trying to live up to his potential after he settles for a job at a restaurant.

Andy accidentally fights with the town's patron saint, Amanda Hayes, who's husband was disabled after a stroke and she's been taking care of him for the past five years. Meanwhile, Jake asks Nina out on a date; Ephram and Bright continue to drift apart; and Harold sets out to come up with his own medical invention.

Andy thinks that Ephram is beginning to doubt getting into Julliard when he applies to a Colorado college as a back-up plan. Harold is also worried about Amy's college career when she tells him that she's not going to the college that Harold had set his hopes on: Princeton. Meanwhile, Andy researches new therapies for Amanda's husband; and Edna and Irv's relationship hits a rough patch.

When Jake confides in Andy that Ephram came to him for an STD test, Andy and Harold decide to try to stop Ephram and Amy from having sex. However, when both Andy and Harold talk to their respective children, Ephram becomes suspicious. Meanwhile, Nina tells Jake about her true feelings for him, then asks him out to dinner; and Bright invites Hannah to the movies.

Ephram, having trouble choosing music for his Julliard audition, goes to Will Cleveland for help. However, things don't go as planned and Ephram, after hurting Will's feelings, has to face preparing for is audition without the help of his mentor. Meanwhile, Bright gets a job at The Firehouse, but gets into a bad situation when the boss finds him and a beautiful co-worker in the storage closet together; and John's music therapy begins to go very well, but Andy can't help but question the results.

Amy and Ephram plan a romantic night together at the Abbott cabin in order to take their relationship to the next step. When they arrive at the cabin, and after their parents worrying about how they'll handle having sex, Ephram and Amy worry that their relationship won't be able to handle the next step. Back in Everwood, Andy and Amanda chaperone Delia and Charlie on a date, but the evening takes a bad turn when Andy assumes he's on a date with Amanda; and Nina gets help from Jake after Sam is hurt ice skating and her feelings towards him begin to change.

Andy struggles to maintain a strict patient-doctor relationship with Amanda, but his feelings for her continue to grow leading him to transfer the case to Dr. Abbott. When Ephram hears that Madison's band will be playing in Everwood, he goes to Bright for advice on whether or not he should see her. Meanwhile, Amy discovers Hannah's family's shocking secret.

After Amanda decides to send her husband to a treatment facility, Andy collapses in front of Harold due to all the added stress of the guilt he's been feeling. Meanwhile, Amy continues to shut out Ephram for lying to her about Madison; and Edna makes Irv a writing room, but her seemingly kind gesture causes a fight between the two.

Jake's ex-girl friend from Los Angeles shows up in Everwood unannounced and Nina comes to the rescue when Jake needs someone to talk to and help get rid of her. Ephram and Amy reconcile and decide to get back together when Ephram promises to be the the new supportive boyfriend she deserves. Meanwhile, Harold and Rose worry that Amy might get her heart broken when she decides to try out for a ballet program in Denver; and Andy accidentally embarrasses Delia in front of her entire hockey team.

Nina stumbles upon Andy and Amanda together, leading her to wonder about Andy and their relationship. Ephram and Amy convince Hannah and Bright to join them on a ditch day in order to have the perfect day after all of the stress of college applications. Meanwhile, Edna and Harold work out their differences when a water pipe bursts in Harold's office.

Amanda and Andy decide to tell Charlie and Delia about their relationship and Charlie's reaction to the news makes Amanda and Andy reconsider their relationship. Amy begins to think that Hannah has a crush on Bright when she turns down going on a date with Topher. Meanwhile, Nina worries how a relationship with Jake might affect Sam.

As Amanda and Andy's relationship begins to work out, they receive news that John, Amanda's husband, has experienced a breakthrough and seems to be recovering better than expected. Meanwhile, Amy learns the real reason that Madison left Everwood; Ephram lands an audition at Juillard; Hannah has to decide whether or not she wants to take the test for Huntington's Disease; and Bright is faced with a sexual misconduct in the workplace accusation.

Ephram runs into Madison while he goes to New York for his Juilliard audition. Amy feels that if she accompanies Ephram to New York, It would endanger his auditions. Meanwhile, Andy, who joined Ephram on the trip, is flooded with memories of his former life, though they quickly vanish when he sees Madison. Also, Bright decides to apologize to every girl he has ever hurt. and Irv and Edna continue to deal with the pain of their breakup.

Before his Julliard audition, Ephram makes plans to meet Madison for coffee. There, he learns about Madison's pregnancy and their child. Upon hearing this, Ephram makes decisions that greatly affect his future. Meanwhile, Amy tries to figure out how the baby will interfere in her relationship with Ephram; and Harold talks to a man whose son may die due to a hunting accident.

Ephram returns from New York and heads for the child services office in an effort to find his baby. But is disappoints to find out that Madison had signed up for adoption with an unknown father. Amy tries to set up another audition at Juilliard for him but because of lot on his mind, Ephram’s audition doesn’t go well. Meanwhile, Andy is shocked to learn the extent of Nina's feelings for Jake. And Hannah arranges a date with Topher.

Jake's younger brother pays him a visit. And he's critical of Nina and of Jake's decision to live in Everwood and suggests that Jake may take an opinion from Andy. Elsewhere, Ephram forgives Amy, but he's not ready to get back together. Meanwhile Amy receives her acceptance letter to Princeton and figures out that her father might have sent her application. There is a conflict between Rose and Harold regarding health issues.

Ephram, in an attempt to raise funds to travel to Europe, sells his music equipment, breaking his father’s heart. Nina can’t figure why Andy has been acting strange around her, but Delia knows exactly why -- he has feelings for Nina. Meanwhile, Bright becomes jealous of Topher when he continues to date Hannah; and Rose begins her cancer treatments.

Mama Joy's shuts down and Nina worries about finding a new job until Jake buys the establishment and asks her to run it. But they have problems in dealing with the situation of their relationship. Ephram prepares to leave Everwood and go to Europe thinking that there is nothing left for him in the town. Also, Andy gives Ephram a special graduation gift that his wife bought years ago. And Bright admits to Ephram that he's starting to see Hannah as more than a friend.

Andy considers accepting a prestigious post with a Chicago hospital; Harold takes it upon himself to give Andy a reason to stay in Everwood; Jake moves in with Nina, and Bright admits his feelings to Hannah. With Ephram in Europe, Andy considers a prestigious position at a hospital in Chicago. Harold tries to give Andy a reason to stay, while Andy mulls over telling Nina how he feels about her, even though she has just moved in with Jake.