The residents of Everwood cope with the death of Colin following his unsuccessful brain surgery operation, which causes the town to pull away from the Brown family. Andy feels guilty over his promise to Colin to not resuscitate him in the event of the surgery's failure, a fact which becomes known to Amy and the rest of the town and leads to a confrontation.
Ephram focuses all his energies on his Juliard audition, which dismays Andy, who would rather Ephram concentrate on extracuricular activities for top college applications. Amy, rather, exhibits a lack of interest college altogether, which worries her mother. As Bright's grades drop, he is kicked off the football team, which Dr. Abbott fears will jeopardize his son's scholarship.
The unexpected arrival of Linda Abbott, who has been travelling and practicing the ways of eastern medicine, throws the Abbott family for a loop. While Edna gloats over her daughter, tensions arise between Harold and Linda when when she wishes to join his practice.
When Andy hires a college student to look after Delia, Delia's new caretaker ends up humiliating Ephram in front of Amy and making him feel like a kid. Dr. Abbott and his sister, Linda, continue to bicker with each other and disagree over their differing medical approaches. Meanwhile, Andy is shocked to learn that Nina is filing for divorce, as he has been consumed by Colin's father's drinking problem.
When Andy extends an invitation to Linda Abbott for dinner, Delia shows her discontent using some very coarse language during the meal. With Madison's reasoning, Ephram is able to determine why Delia is acting out. Meanwhile, Amy's therapist suggests to Dr. Abbott that his daughter should take medication for her escalating depression, but Dr. Abbott decides he won't write out a prescription.
Andy tries to help a reverend, who is rapidly going blind, but neither the doctor nor the reverend's wife can persuade the reverend to put his faith in medicine instead of the lord.
Andy, Linda, Edna, and Harold Abbott join forces to assist a group of injured miners when a mine collapses, including Ephram's mentor, Will, Dr Abbott's neighbor, Daniel, and Ellie, a patient of Andy's, during which time Andy must confront one of his fears as the doctors utilize their decisive medical skills in moments of crisis.
The town begins to think a car mechanic is a seer when he manages to diagnosis a young patient of Andy's that Andy has misread. Colin asks Madison to tell him where their relationship stands, while Amy goes to see Linda Abbott, but ends up stealing her prescription pad. The mechanic then warns Dr. Abbott that his daughter may be headed for trouble. Meanwhile, Edna finds out what's been keeping Linda from committing to Andy.
Andy continues to woo Linda Abbott, prompting Harold and Edna Abbott to advise that he back down, at which time Linda reveals to Andy she's HIV positive. Bright advises Ephram on how to win Madison's heart by being aloof, but the effect is that she breaks up with her boyfriend. Meanwhile, Amy is intrigued by the compassion of a sensitive bad boy who has rolled into town.
Dr.Brown finds out that Ephram is dating Madison and forbids them to continue; Amy brings her boyfriend home for Thanksgiving dinner and ends up running away from home after she and her father get in a fight.
Delia and Ephram deal with the fact that Andy has begun dating Linda Abbott, a point especially hurtful to Delia because of his explicit promise not to do so. Meanwhile, Amy moves in with Edna and Irv, a move which worries and upsets Rose and Dr. Abbott.
Andy tries to come to the aid of a wrestler who is bulimic obssessed with winning at all costs. Trouble finds Bright when he engages in fisticuffs with Amy's new boyfriend. Meanwhile, Ephram thinks Madison is balking at being spotted with a high school kid, while Linda fears Andy may be avoiding intimate contact because of her HIV status.
Amy gets in to a major argument with Tommy, which causes her to forget her father's birthday dinner. Ephram plays one of his songs for Madison, but her lack of enthusiasm for the material leads to an argument between them. Meanwhile, Andy gets an earful from Nina when she thinks he's abandoned their friendship while pursuing Linda.
When Madison informs Ephram that her roommate is going to be out of town for a bit, he gets a different impression than what she had intended. Amy asks Andy to give her a prescription for birth control pills, as she plans to have sex with Tommy, which leads Andy to realize that he should be open with Ephram and Delia about Linda staying overnight at their house.
Ephram is torn up inside when he tells Madison that he loves her, but the surprise of his announcement doesn't translate into the same feelings towards him. Andy, Ephram, and Ephram's piano teacher, Will, attend a Jazz piano competition in Boulder, leaving Delia in Linda's care for a sleepover. Meanwhile, fearing something in her relationship with Tommy has gone awry, Amy tells him she wants to break up.
Bright helps Ephram aquire a fake I.D. to go see Madison's band perform in a bar, but while at the show, Ephram ends up getting into a bar fight. Andy helps Nina cope with the impact of receiving her divorce papers, which concerns Linda. Meanwhile, Amy attends a house party with Tommy, but her peace with Colin's death is shattered when Tommy has a near-fatal drug overdose.
After returning home, Amy has a tough time trying to fall into her old life, as tensions continue to exist between her and her parents and she is ignored by her old friends. Meanwhile, Ephram worries that Madison is about to break off their tumultuous relationship, while Andy testifies on Nina's behalf during her divorce proceedings.
Ephram and Madison decide, to Andy's chagrin, that now that they've stopped dating, it would be better if Madison went back to being Delia's babysitter. Meanwhile, Bright awaits letters from colleges, while Linda assists Amy when she considers stopping the use of her antidepressant prescription.
Bright tries to cool Amy off of the idea that Ephram is ready to date again when she confesses that she's got feelings for Ephram. Meanwhile, Delia's inadvertent reveal of Linda's HIV status leaves Dr. Abbott's patients angry, and him with potential claims of malpractice. It also upsets Ephram, who believes Andy kept the information a secret from him.
Amy and Ephram decide to go the prom together like two friends hanging out, but she hasn't told Ephram that she has some feelings for him. She loses her chance when they see Madison and Amy becomes aware of how it's triggered Ephram's emotional wounds. Meanwhile, Andy's medical mentor asks Andy to perform a dangerous brain operation on him, while Linda contemplates leaving Everwood.
Amy tags along with Ephram to Boulder for his Juilliard audition and opens up about her rekindled feelings for him. Andy tries to explain the degree of difficulty in Dr.
Ephram's feelings are split when, after winning acceptance into Juilliard's summer track, Amy tells him she doesn't want him to leave. Meanwhile, Andy learns some troubling family information, while Dr. Abbott, despondent over his practice's insurance woes, decides to starts his own bagel business.