Following Amanda's decision to send her husband to a world-renowned treatment facility, Andy 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 infidelity with Amanda. Meanwhile, Amy continues to give Ephram the cold shoulder for lying about Madison, and Edna builds a writer's room for a depressed Irv, but it doesn't go over well and they consider separating.
When Jake's girlfriend from Los Angeles arrives in Everwood unexpectedly, Nina comes to his rescue with a shoulder to lean on and the possibility of more. Meanwhile, Harold and Rose worry about Amy after she sets her mind to auditioning for a rigorous ballet program in Denver, and Andy unintentionally humiliates Delia in front of her hockey team.
Andy must face the repercussions of his affair with Amanda when Nina accidentally discovers them together and questions Andy's character. Meanwhile, Ephram and Amy convince a reluctant Hannah to ditch school for the day and take Bright along for the ride. Harold and Edna are forced to push their hostile feelings for one another aside when a medical emergency leaves them with no other choice.
Andy and Amanda decide that it's time to tell Delia and Charlie about their relationship before they hear about it elsewhere, but Charlie's emotional reaction makes them question what they're doing. Meanwhile, when Hannah doesn't jump at the opportunity to go on a date with a really cute guy from school, Amy is convinced that Hannah is misguidedly saving herself for Bright, and Nina questions whether Sam is going to be hurt again if her relationship with Jake doesn't work out.
Just as they've become somewhat comfortable with their new relationship, Andy and Amanda receive word that Amanda's husband, John, has experienced a miraculous breakthrough in his recovery. Meanwhile, Amy learns the truth about why Madison really left town, an elated Ephram is offered an audition at Julliard, Hannah questions whether she's emotionally prepared to take the test for Huntington's Disease, and Bright is accused of sexual misconduct in the workplace.
Feeling conflicted over the recent turn of events and not willing to jeopardize Ephram's Julliard audition, an angst-filled Amy tells Ephram that he should take Andy to New York instead of her. In New York, Andy struggles with memories of his former life and the desire to tell Ephram the truth about Madison. Fate plays a hand when Ephram runs into Madison in Manhattan and they make plans to see each other, causing Andy to take matters into his own hands.
On the morning of his Julliard audition in New York, Ephram makes plans to meet up with Madison for coffee, only to have his entire world come crashing down around him when she tells him that she was pregnant with their child. This devastating revelation causes Ephram to make decisions that will alter the course of his life. Meanwhile, back in Everwood, Amy can't quite make heads nor tails of what will happen to her relationship with Ephram once he learns the truth about Madison, and Dr. Abbott counsels a man whose son may die as a result of a hunting accident.
After returning from New York feeling lost and confused and needing Amy for support, Ephram considers his options in the wake of Madison's life-altering revelation. Meanwhile, Andy is a little stunned upon learning the extent of Nina's feelings for Jake and, with a little encouragement from her friend, Bright, Hannah decides to go on a date with a smitten Topher.
When Jake's little brother comes to visit and confides he doesn't see a future for Jake and Nina, Jake seeks counsel from an unlikely source... Andy. Meanwhile, Amy is accepted into Princeton, but assumes her father was the one who secretly sent in her application, and Ephram and Amy make plans to spend an evening together, further confusing the status of their relationship.
Ephram makes a bold move -- and breaks his father's heart in the process -- in an attempt to raise money for a plane ticket to Europe. Meanwhile, Nina can't quite put her finger on why Andy has been acting strangely of late, whereas a more perceptive Delia comes right out and asks her father whether he has feelings for Nina, and Bright's green-eyed monster makes an unexpected appearance when Hannah goes to prom with Topher.
Feeling there is nothing keeping him in Everwood and desperately needing distance from Andy, Ephram prepares to leave family and friends behind for a new life in Europe. However, he's caught off-guard and questions his plans when Andy reveals the secret that Amy has been keeping from Ephram. Meanwhile, Nina and Jake contemplate going into business together, but the stress on their relationship proves a big obstacle to overcome, and Bright confesses to Ephram that he has developed feelings for Hannah.
With Ephram gone and no longer feeling any significant ties to Everwood, Andy consults with Delia and contemplates accepting a prestigious position with a Chicago hospital. Uncharacteristically upset over this bit of news, Harold takes it upon himself to give Andy a reason to stay. Meanwhile, Jake moves in with Nina, causing Andy to question whether he should rock the boat by telling her how he really feels, and Bright finally admits his feelings to Hannah.
At the end of last season, Andy left Nina speechless by finally declaring his love for her, and Ephram decided to make a clean break from his troubles in Everwood by moving to Europe. In the season premiere, Nina will choose between the two men she loves - Andy and Jake. At Delia's behest, Ephram makes an emotional return to Everwood just in time for an unexpected wedding; Bright and Hannah are reunited after their first kiss and a summer spent apart; and Amy and Rose find that Rose's cancer has driven them apart rather than brought them together.
Andy learns that Ephram has no intention of moving back home, while Bright invites Ephram to move in with him and Reid. Meanwhile, Hannah begins to worry about the long term possibilities for her relationship with Bright after he shares his "three dates and out" policy; Harold suspects Andy is up to something after he frequently goes missing from the office; Nina and Jake have the grand opening for their new restaurant; and Ephram and Amy finally confront the unspoken fate of their relationship.
As if adjusting to college life and the news that her secret crush, Reid , is gay weren't enough to handle, Amy learns that Ephram is going to be a regular fixture in her life now that he's moved in with Bright and Reid. Meanwhile, Andy, Nina and Jake attempt to move on with life after Nina decides which man she loves. Bright and Ephram take Hannah to a college party.
Ephram begins giving piano lessons to a 14-year-old piano prodigy, Kyle, but Ephram soon realizes that the music awakens difficult memories from last year. Meanwhile, Dr. Brown advises a brain tumor patient and his wife; Harold and Rose await the latest cancer test results while dealing with the stress of a mayoral reelection; and Delia informs her father she wants a Bat Mitzvah.
On a camping trip with Andy and Harold, Ephram reveals the true reason he returned to Everwood and Bright contemplates a sex-free relationship with Hannah after she tells him that she doesn't believe in pre-marital sex. Meanwhile, Amy grows even more emotionally confused when Reid asks her to go with him to a Halloween fundraiser, Jake and Edna's working relationship is put to the test when Edna questions his work ethic and Ephram learns more about his mysterious piano student, Kyle.
In hopes of mending Andy and Jake's friendship, Nina suggests the two men go to counseling together. Meanwhile, Andy breaks the news to Ephram that Amy may be seeing someone new; Harold helps Rose find new direction after losing the mayoral reelection campaign; and Ephram realizes that Kyle's life may be more complicated than he originally thought.
Hannah's mother pays an unexpected visit to Everwood to tell Hannah that her father has passed away. Elsewhere in Everwood, Ephram stifles his feelings for Amy while forced to watch her relationship with Reid grow more serious; Andy advises a patient who desperately needs a kidney transplant, but refuses to accept one from his daughter; and Bright is at a loss at how best to help Hannah through this difficult time.
Changes are happening as Hannah gets ready to leave for Minnesota with her mother and Bright and Amy are having deal with the loss of their best friend, and Bright's girlfriend. Amy also has to deal with the lack of contact from Reid as he follows through on his promise to end his relationship with Amy. The adult males go through a dangerous time as they take on risky adventures. It starts with Jake and his friend Cliff going out on a bike trip that turns dangerous. Then Andy and Harold decide to go seize the day and go skydiving.
A very-much-in-love Ephram discovers that he has become a "girlfriend" to Amy, but the friendship is threatened when a moment of intimacy leads to them waking up together the next morning. Meanwhile, Nina grows suspicious of Jake's recent strange behavior, which is furthered when his brother shows up unexpectedly; Andy is worried when Delia takes up with the popular girls in school; Bright tackles Hannah's low self-esteem issues; and Rose drops some startling news on Harold.