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.
With a week having past since they slept together, Ephram and Amy must figure out what this new development means for their future, and Nina and Jake face the biggest obstacle of their relationship yet. Meanwhile, Irv's brutally honest description of Andy in his debut novel causes Andy to take a long look in the mirror, and Ephram realizes that he and Kyle may have even more in common than he originally thought.
Amy's new college professor encourages her to get involved with Planned Parenthood. When Amy tries to get Hannah to volunteer as well, it leads to a serious rift between the friends. Harold and Rose consider adopting a child from Africa. While Irv is on his book tour, Edna winds up in the hospital and Andy comes to the rescue. Ephram's sadness over his relationship with Amy and his sudden lack of direction in life is made worse by the news that his piano teacher, Will Cleveland, has died.
Although Jake is back from rehab and going to 12-step meetings every night, Nina realizes she has no idea how to deal with his recovery. Andy cancels his first Internet date to give Nina emotional support. Amy tries to impress Professor Fields by using her father, which results in Dr. Abbott lying to his daughter about his past. Ephram encourages Kyle to meet with his long-absent father, opening old wounds for Ephram regarding his own son. When Delia asks Andy to listen to the rough draft of her Bat Mitzvah speech, he is deeply touched by her memories and her message.
Ephram talks Kyle into accepting the invitation of a pretty classmate to go to a school dance, but when Kyle has a terrible evening, Ephram finally faces his suspicions that Kyle may be gay. Feeling that he has made things worse for Kyle, Ephram turns to Amy and Andy for advice. Ellie, an girl with a family history of breast cancer, asks Andy to perform a preventative mastectomy, and Harold is appalled at Andy's decision. In an attempt to put the excitement back in her relationship with Bright, Hannah throws a Hawaiian luau for two.
Ephram plans to transfer to Colorado A&M, but Andy counsels him not to choose a school just to be near Amy. Knowing that Ephram regrets his lost opportunity at Julliard, Andy sets up a meeting for him with a concert pianist and it helps Ephram decide what he wants to do. With things starting to feel back on track, Nina tells Andy she's proposing to Jake. Finally, Bright is unable to admit to Hannah that the absence of sex in their relationship is hard for him. After they quarrel, Bright runs in to Ada and makes a terrible mistake.
Ephram learns that Bright cheated on Hannah and is outraged. When Ephram confides in Amy, she also confronts Bright and convinces him that he must tell Hannah the truth. Harold asks Andy to protect his lie on the adoption application regarding Rose's cancer. Irv takes Edna along on his book tour appearance in San Diego, and they spend time with Irv's daughter Cassie. Reid's desperate actions lead to terrible news from his medical school advisors.
Devastated by his expulsion, Reid tries to commit suicide. Ephram rescues him, but can't forgive himself for missing the signs of Reid's depression. Andy and Nina are caught in a compromising situation when Nina admits she may still have feelings for Andy. Trying to win Rose's forgiveness, Harold buys her a necklace, but Bright takes the necklace to give it to Hannah as an apology for his affair.
Just out of the hospital, Reid asks Amy out on a date. Amy talks a reluctant Hannah on a double date with Amy's friend Nick, leaving Bright to deal with his pain and jealousy. Delia panics when her Bat Mitzvah falls on the same day as the birthday party of the most popular girl at school. Nina tries to deal with her confusing emotions over Andy and realizes she will have to make a decision when Jake asks her to move to Los Angeles.
Andy, Ephram and Delia are all shocked by a visit from Andy's estranged father, whom they haven't seen for 15 years. Ephram and Amy take Bright out to celebrate his 21st birthday, but Bright drinks too much, falls through a window and ends up in the hospital. Hannah rushes from her date with Nick to be at Bright's side. Nina decides to move to Los Angeles with Jake, which devastates Andy. Irv and Edna decide to buy an RV and spend their retirement traveling the country.
The whole town gathers for Irv's funeral. After the funeral, Amy begins to rethink her relationship with Ephram. Ephram decides he should tell Nina that Andy has bought an engagement ring for her before she makes the final decision to leave Everwood with Jake. Finally, when Andy's father announces that his visit is over, he and Andy have an honest and long-overdue conversation about their feelings for one another.
While packing up her house and preparing to leave Everwood with Jake, Nina tells Hannah that she knows Andy bought an engagement ring for her. Hannah convinces Nina to sneak into the house while the Browns are out to get a look at the ring. Later, Jake finds out about the ring and confronts Andy once again about his feelings for Nina. At Delia's Bat Mitzvah, Amy watches Ephram with his new girlfriend Stephanie and realizes her feelings for Ephram are still strong. And when one of Harold's patients leaves her baby on the Abbott's doorstep, Harold wrestles with the ...
After their house has been sold, Nina and Sam temporarily move in with the Browns. Wanting to take care of an unresolved issue in his life before he can propose to Nina, Andy takes a mysterious trip. Bright learns that Hannah has received a scholarship to Notre Dame and is devastated at the thought that she may accept it. Edna upsets Harold and Rose when she reveals her plans to leave Everwood. Delia is thrilled with Andy's belated Bat Mitzvah gift. Finally, when Amy tells Stephanie that she plans to tell Ephram about her feelings for him, Stephanie steps up her game ...