Ephram and Amy are reunited after a long summer spent apart while Ephram attended Julliard's summer program in New York... but Amy's euphoria is quickly replaced with paranoia after she notices Ephram acting distant. Meanwhile, Andy is plagued by guilt over whether he made the right decision concerning Madison's pregnancy; and Dr. Abbott befriends the town's newest citizen, Jake Hartman, who turns out to be a doctor from California looking to open a new practice in Everwood.
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. Andy contemplates telling Ephram about Madison's pregnancy. Meanwhile, Rose naively agrees to help Bright find his true calling after she discovers that he hasn't enrolled for college classes and is in fact leading a life of total leisure; Dr. Jake Hartman creates a marketing blitz for his new practice that threatens to push Dr. Abbott over the edge; and Nina takes in...
Ephram regrets promising Nina that he would watch over Hannah at school, especially when her constant presence interferes with his time alone with Amy. Amy befriends Hannah out of a sense of charity, but soon finds Hannah so refreshing that a real friendship develops. Meanwhile, Andy tries to ignore the tension between Dr. Abbott and Edna, but his attitude forces Edna to quit and go to work for Dr. Hartman. Andy treats a 13-year-old patient whose mysterious injuries cause Andy to suspect the boy's mother of abuse.
Andy finds himself at a loss over what to do when Delia naively stumbles upon Nina's vibrator and starts asking questions. Meanwhile, Ephram attempts to write Amy a love letter to show her the extent of his feelings; Amy makes it her mission to make new best friend Hannah popular; and Harold and Rose question Bright's euphoria over being selected "employee of the month" and decide it's time for some parental intervention.
Andy puts his foot in his mouth by picking a fight with Everwood's patron saint, Amanda Hayes, who, unknownst to Andy, has been caring for her profoundly disabled husband for the past five years. Meanwhile, Jake surprises Nina by asking her out on a date; Ephram and Bright realize their friendship may have grown too far apart to salvage; and neurotic-as-ever Dr. Abbott struggles to come up with a medical invention after learning that Dr. Brown and Dr. Hartman have successful inventions of their own.
Andy worries that Ephram is beginning to question himself and his chances of getting into Julliard after he applies to a college in Colorado as a back-up plan. Similarly, Harold has concerns of his own when Amy informs him that she's not applying to the school they always dreamed of her attending, Princeton, because it would take her too far away from Ephram. Meanwhile, Andy jumps head first into helping Amanda and her disabled husband with a new therapy involving music, but it may be too much and too fast for Amanda; and Edna and Irv's marriage hits a rough patch ...
When Jake surreptitiously informs Andy that Ephram came to him for a STD test, Andy and Harold decide the best plan of action is to convince Ephram and Amy to hold off on sex. Of course, when Ephram realizes it's no coincidence that he and Amy both had a heart-to-heart with their fathers on the same day and informs her of his suspicions, Amy feels betrayed that Ephram didn't tell her about the test beforehand.
Struggling to select the music program for his Julliard audition tape, Ephram seeks guidance from his music teacher and mentor, Will Cleveland, but faces losing one of the most important relationships in his life after he regretfully hurts Will's feelings. Meanwhile, Andy and Amanda experience a miraculous breakthrough in their music therapy with Amanda's husband, but Andy quickly begins to question whether their celebratory mood is premature; and Bright continues down his unfortunate path of apathy by getting fired from his job - for getting intimate with a waitress ...
Ephram and Amy decide they're ready to take the next step in their relationship with romantic plans to meet at the Abbotts' lake house, but the enormity of the situation proves too much for the couple to handle. Meanwhile, Andy and Amanda play chaperones for Delia and Charlie's pizza date, but the evening turns out to be more of a date for the two adults, who realize their mutual attraction is wrong. Finally, Nina reevaluates her feelings for Jake after he comes to her rescue.
Realizing that his feelings for Amanda are only growing stronger despite his best efforts to maintain a platonic friendship, Andy decides it's in both of their best interests if he refers her husband's case to Dr. Abbott. Upon hearing news that Madison's band is performing in town, Ephram seeks guidance from Bright, signaling a thaw in the boys' chilly relationship as of late. Finally, Amy's curiousity unearths Hannah's family secret.
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.