As the season opens where last season's cliff-hanger left off, Nina is forced to choose between Andy and Jake, but will she pick the man she truly loves? At Delia's request, Ephram returns to Everwood just in time for a wedding. Meanwhile, Bright and Hannah see each other for the first time after a summer apart; Amy and Rose's relationship suffers due to Rose's cancer; and Amy falls for Reid, a medical student at her college.
Andy is devastated when he learns that Ephram won't move back home but is going to live with Bright and Reid instead. Hannah begins to reconsider her relationship with Bright when he tells her about his "three dates and out" rule. Meanwhile, Nina and Jake open Sam's to a mediocre response from the town; Harold is suspicious of Andy when Andy leaves the clinic frequently throughout the day; and Ephram and Amy talk about their relationship.
Amy, trying to adjust to college life and coming to terms with the fact that her crush, Reid, is gay, is thrown another punch when she learns that Ephram will be living with her brother and Reid. Nina and Jake try to move on with their lives after Nina makes her decision; and Bright and Eprham take Hannah to a party.
To make money, Eprham begins giving piano lessons to a Kyle, a 14-year-old piano prodigy, but the lessons stir up old emotions in Ephram. Meanwhile, Andy meets with a brain tumor patient and his wife; Delia tells Andy that she wants a Bat Mitzvah; and Harold and Rose deal with the stress of test results and the results of the Everwood mayoral election.
While camping with Andy and Harold, Ephram reveals the real reason he came home. Back in Everwood, Bright considers a sexless relationship with Hannah when he learns that she doesn't believe in pre-marital sex. Amy becomes confused by Reid's actions when he invites her to go to a Halloween fundraiser with him; Edna and Jake square off over Jake's work ethic; and Ephram learns more about Kyle's life.
Songs: Deb Talan -- Forgiven
Wanting to fix Andy and Jake's friendship, Nina suggests that the men go to counseling to sort out their differences with a professional. Meanwhile, Andy tells Ephram that Amy might have a boyfriend; Rose deals with losing the mayoral election; and Ephram continues to learn the about the complications in Kyle's life.
Hannah's mother arrives in Everwood to tell her daughter that her father has died, and Bright tries step up to help Hannah through this hard time. Ephram has a hard time dealing with Amy and Reid's new relationship while Andy has a hard time finding a kidney donor for a patient when the patient's daughter refuses to donate a kidney.
Bright and Amy try to deal with Hannah leaving and each of them take her departure harder than they expected. Jake and Cliff, one of Jake's friends, go on a high-risk, high-skill level bike ride, but their excitement is cut short when the trip takes a near fatal turn. Meanwhile, after hearing about Jake's daredevil trip, Andy and Harold decide to go skydiving; and Reid pulls away from Amy at Ephram's request, leaving Amy even lonelier.
Songs: Hem -- Pacific Street
Though still madly in love with Amy, Ephram, much to his chagrin, has become more of a "girlfriend" to Amy than a boyfriend. Their new-found friendship takes a romantic turn when they end up waking up together. Nina becomes suspicious of Jake's strange behavior, and begins to think that something is up when Jake's brother comes to Everwood. Meanwhile, Delia becomes friends with the popular girls at school; Bright tries to help Hannah's low self-esteem; and Rose breaks startling news to Harold.
Amy and Ephram try to sort out their relationship and future after they sleep together. Jake and Nina's relationship hits a bump when Nina learns about Jake's addiction to prescription drugs. Andy re-examines his life after reading Irv's description of him in Irv's novel. Meanwhile, Amy meets a cool, new teacher at Colorado A&M and Ephram spends more time with Kyle.
Ephram falls deep into a depression when he can't figure out his relationship with Amy. He only gets more depressed once he hears that Will Cleveland, his former piano teacher and mentor, has passed away. Bright tries to cheer him up, his style, by taking him to a college keg party, but Ephram doesn't respond to the girls hitting on him and decides to just play video games instead. After urging from a new professor, Amy decides to get involved with Planned Parenthood, but this creates a rift between her and Hannah when Amy tries to get her to volunteer as well. Meanwhile, Edna suffers a panic attack and Andy takes her to the hospital; Harold and Rose decide to adopt a child, but get caught up in the complexities of doing so; and Delia continues to grow more rebellious.
Andy goes to a Rabbi, Josh Stein, for help in planning Delia's Bat Mitzvah. Despite bringing back feelings about his own lost son, Ephram supports Kyle as his estranged father returns to town. Andy tries to get a date with a woman over the Internet, but is forced to postpone several times, including once to help Nina through an emotional crisis brought on by Jake's recovery. Meanwhile, one of Amy's college professors consults Harold about a medial procedure.
An eighteen-year-old girl comes into Andy's clinic to be checked for breast cancer because it runs in her family. When the results come in, the girl and her older sister, who has had a double mastectomy due to breast cancer, return to see them. Meanwhile, while out on a date, Bright and Hannah are forced to call Harold after something happens to the both of them and Kyle tells Ephram that he no longer wants piano lessons.
Andy and Jake's early morning get-together is interrupted when a drunk driver crashes into a pole in front of them. Later, Jake goes to the hospital in order to talk to the driver about addiction. Meanwhile, Amy introduces Hannah to her college friends, Reid has a serious talk with an academic adviser, and Harold meets a woman from Rose's cancer support group.
Songs: The Submarines -- Peace and Hate
Bright makes a mistake that threatens his relationship with Hannah; Kyle gets a Juilliard audition and Andy, knowing this news triggers feelings of regret in Ephram, encourages his son to try another music school; Nina tells Andy she wants to propose to Jake; and Amy reluctantly brings Laurie to her parents' house for dinner.
Ephram discovers the truth about what happened between Bright and Ada and wonders what he should do with the potentially devistating information. Irv's estranged daughter arrives at his book signing, much to the chagrin of Edna. Meanwhile, Reid gets devastating news from his advisor; Harold begs Andy not to tell the social worker from the adoption agency about Rose's cancer; and Amy tries to fix her friendship with Hannah.
Ephram finds Reid unconscious after overdosing on pills in a failed suicide attempt. Bright, feeling miserable after their breakup tries to fix things between him and Hannah. Meanwhile, Laurie suggests that Amy go to Washington D.C. for a conference, but when Amy meets Laurie's daughter, she re-evaluates her opinion of her professor; and Nina, struggling with her feelings for Jake, discovers that she still has feelings for Andy.
Returning home, Reid, strangely cheerful, finds Bright miserable and dejected, then finally gets the courage up to ask Amy out. The date become quadruple when Amy gets Nick to make his move on Hannah. Meanwhile, Harold treats a schizophrenic pregnant woman, whose husband has a scary physical condition; and Delia asks Andy to postpone her Bat Mizvah because a friend is having their party on the same day.
Andy's father shows up shockingly at the Brown house after 15 years of absence. Bright gets drunk in his 21st birthday party and ends up getting rushed to the hospital after falling through a window. As she learns about the incident, Hannah leaves Nick to be with Bright. Meanwhile, Nina's decision to move to Los Angeles with Jake devastates Andy. Irv and Edna buy an RV to travel around the country after their retirement, but an unexpected tragedy cuts their retirement plans short.
Nina's struggle to figure out who he loves more between Andy and Jake takes new development when Ephram tells her his father bought an engagement ring. Memories brought back to Amy about Ephram and her, making her revaluate everything about each other. Learning about something he and his father are both involved, Andy and Gene wind up to have a long conversation about their feelings for one another. Figuring out not everything is lost, Bright and Hannah establish a new friendship.
While packing to leave Everwood, Nina confides in Hannah that she knows Andy bought an engagement ring, and Hannah convinces her to sneak into the Brown's house to take a look at it. But when Jake finds out about the ring, he goes to confront Andy about his feelings for Nina. Meanwhile, after seeing Ephram with his girlfriend, Amy realizes that her feelings for him have never really gone away; a patient of Harold's leaves her baby at the Abbott's doorstep; Bright learns about Hannah's college plans; and Edna reveals her plans to leave to Harold and Rose.
With their house being sold, but their new house not ready for them to move into, Nina and Sam temporarily move in with the Browns. Andy, wanting to take care of unresolved issues from the past, takes a road trip before proposing to Nina. Meanwhile, Bright learns that Hannah got a scholarship to Notre Dame and is devistated when he learns that she might take it; Andy becomes increasingly attached to the baby girl left on his doorstep; Delia is elated with Andy's late Bat Mizvah gift; Amy reveals her feelings for Ephram to Stephanie, who won't loose Ephram without a fight; and Harold and Rose deal with the news that Edna is leaving Everwood.