After his wife is killed in a car accident, Dr. Andrew Brown moves his 15-year-old son, Ephram, and 9-year-old daughter, Delia, to the idyllic environs of Everwood to make a new start. In the opener, the relocation sparks harsh words and hurt feelings between the emotionally distant father and his neglected son, despite Andrew's attempts to reconnect with the teen. The good doctor also runs afoul of the town's only other physician when he decides to open his own practice---right across the street from his rival's office.

Andy and Ephram's fragile relationship is further strained when it appears that Andy is once again putting work before family. Meanwhile, as the town of Everwood celebrates its annual Fall Thaw Festival, Ephram's interest in Amy continues to blossom. Although Bright tells Ephram that Amy is using him just go get his father to get Colin out of coma. Delia gets into trouble at school for questioning her teacher's antiquated rules.

Approaching the anniversary of his mother's death, Ephram confronts a repressed memory of his father cheating on his mother, causing an even bigger rift between father and son that eventually leads to a firestorm of emotions. Meanwhile, Amy grows concerned that Colin might not be recovering as well as everyone thinks when he gets violently ill on one of their dates. Amy tells her father who later tells Doctor Brown which causes the Harts to dismiss Andy from being their family doctor and causes a feud between Amy and her father.

Dr. Brown faces one of the toughest moral decisions of his career when a distraught pregnant teenager (guest star Kate Mara) and her father (guest star Kevin Tighe) come to him for guidance about terminating her pregnancy. Meanwhile, Ephram is humiliated in front of the entire school when his date for the Spring Formal ditches him at the dance to make-out with her boyfriend. Lastly, Amy and Colin (Mike Erwin) have a huge fight when she chooses to console Ephram against Colin's wishes.

In the second season opener, the town of Everwood deals with the aftermath of Colin's unsuccessful surgery, as he is now dead. The Brown family begins to feel ostracized by the town due to Colin's death. Meanwhile, a saddened Andy feels guilty of not doing his very best as regretting now over his promise to Colin of not resuscitating him if the surgery goes wrong. Amy and the rest of the town find out about this matter and confront Dr. Brown over it.

Ephram and Bright conspire to get Ephram a fake I.D. so that he can get into a bar to see Madison perform with her band. Meanwhile, Nina leans on Andy for emotional support after she is served with divorce papers, but the genuine affection between the two raises a red flag for Linda; Harold and Rose (guest star Merrilyn Gann) schedule a meeting with Amy's guidance counselor after receiving her less-than-stellar report card. Finally, Tommy (guest star Paul Wasilewski) takes Amy to a party where she finds closure over the loss of Colin (guest Mike Erwin), but the evening takes a life-threatening turn.

Ephram is on cloud nine after being accepted into Julliard's summer program, but his emotions are sent into a tailspin when Amy shares her feelings for him and asks that he stay in Everwood for the summer. Meanwhile, Dr. Abbott's family thinks he's gone off the deep end when he decides to open a bagel shop in response to losing his malpractice insurance, and Andy learns a shocking revelation about his family.

Ephram reveals information about his dad to Nina that surprises her and adds a new twist to her inner Andy-or-Jake struggle; Andy finds more of a connection with his dad (guest star Charles Durning), who's still in town; Amy and Ephram recall a moment from their past that helps Amy realize that Ephram is always there for her. Lastly, Hannah and Bright come together as friends, realizing that there's still a close bond between them.