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.

Andy is concerned that Ephram needs more extracurricular activities to get into a top college, but Ephram is only focused on his Julliard audition, which has surprising results. Amy's lack of interest in college preparation alarms her mother more than her father. Bright's poor grades get him kicked off the football team, threatening the scholarship his father believes may be his only chance to get into a decent school. Meanwhile, Andy tries to help a cheerleader (guest-star Kristen Bell) with ruptured breast implants, who cares more about looking good than her own health.

Andy's well-intentioned plan to give Ephram more free time by hiring college student Madison Kellner (guest star Sarah Lancaster) as a caretaker for Delia ends up making things worse when Madison treats Ephram like a child, as well and embarrasses him in front of Amy. Meanwhile, Andy's concern for Colin's alcoholic father (guest star Michael Flynn) blinds him to Nina's struggles with her divorce proceedings. Dr. Abbot continues to clash with his sister, Dr. Linda Abbott, when she tries to take over his office and the difference in their personalities and medical philosophies becomes alarmingly clear.

When Andy invites Linda Abbott over for dinner to discuss a patient, Delia lashes out through foul language, but it is an enlightened Ephram who figures out the cause of his sister's bad behavior, thanks to insight provided by Madison (Sarah Lancaster). Amy's depression deepens, but when her therapist recommends medication, Dr. Abbott refuses to write a prescription to help his daughter cope with Colin's death.

Dr. Abbott suspects that Linda and Andy like each other more than they should, so he decides to set his sister up with more appropriate suitors. Meanwhile, Ephram finally has the courage to tell Amy how he really feels about their relationship, but he is confused by his feelings for Madison, who comes to the rescue when Ephram needs help to pass his driving test. Meanwhile, Andy tries to help the soon-to-be-remarried Reverend Keyes (guest-star Tim DeKay) cope with his impending blindness, but the minister would rather leave his fate to God than attempt a new treatment that might save his sight.

When a coal mine collapses, Dr. Brown, together with Edna, Linda and Harold Abbott, rush to the scene to assist their neighbors. One miner is Will Cleveland (guest star James Earl Jones), a jazz pianist who has recently become Ephram's mentor. The other is Abbott's next door neighbor (guest star Beau Bridges), whose outrageous building plans Harold has tried to thwart. The third one, Andy's patient Ellie Beels (guest star Kirsten Nelson), who has been trying to conceive a baby. All three doctors utilize their special skills under terrible conditions, but it is Andy who must confront his biggest fears in order to save lives.

When Phil the mechanic (guest star J.K. Simmons) correctly ""diagnoses"" meningitis rather than flu in Andy's young patient, the town begins to believe he is a seer. Ephram confronts Madison about his feelings for her. Amy agrees to see Linda Abbott for help, but out of desperation, steals her pad to forge a prescription for anti depressants, forcing Harold to heed Phil's warning about his daughter's condition. Meanwhile, Edna learns the disturbing truth about why her daughter does not want to pursue a relationship with Dr. Brown.

Dr. Brown courts Linda Abbott despite Edna's and Harold's insistence that he's wasting his time, but Andy persists, forcing Linda to tell him that she is H.I.V. positive. Bright tells Ephram he can win Madison's affections by ignoring her, but the plan goes awry when she breaks up with her boyfriend. Amy meets a flirtatious and attractive town bad-boy, Tommy Callahan (guest star Paul Wasilewski), whose compassion for her problems touches her heart for the first time since Colin's death.

Horrified to discover that Ephram and Madison are involved, Dr. Brown stops short of firing her, but Madison decides to quit leaving the Browns to a very unhappy holiday, especially when Delia discovers another troubling relationship - between her father and Linda Abbott. Stressed by Thanksgiving with his cantankerous mother-in-law (guest star Betty White), Dr. Abbott reacts badly when Amy brings Tommy (Paul Wasilewski) to Thanksgiving dinner. Finally pushed to the breaking point, Amy runs away from home.

When Andy's relationship with Delia is threatened after he breaks his promise not to date Linda Abbott, he decides to take his daughter on a special bonding trip to regain her trust. Andy is also surprised by Ephram's emotional reaction to the relationship with Linda. Meanwhile, Andy finds himself in a tough spot when a woman patient wants to get pregnant through in-vitro fertilization with sperm from her first husband, who is now dead, but her second husband is having a real problem over the matter. The Abbott family is still in turmoil when Amy decides to live with Edna and Irv, rather than playing by her parents' rules.

Dr. Brown tries to intervene when a bulimic high school champion wrestler (guest star Douglas Smith, Gregory Smith's brother) puts his life in jeopardy for an important tournament. Bright is suspended from school after he fights with Amy's boyfriend Tommy (Paul Wasilewski). Linda Abbott suspects that that Andy is reluctant to move their relationship to a more intimate level because of her HIV status. Finally, Ephram is convinced that college student Madison is embarrassed to be seen with him.

Caught up in her first fight with Tommy (guest-star Paul Wasilewski), Amy's reconciliation with her father goes awry when she forgets his birthday dinner. Madison lies to Ephram about liking a love song he wrote, which leads to a fight when she refuses to show the song to her band. Nina finally confronts Andy about neglecting their friendship to spend time with Linda.

Ephram gets the wrong idea when Madison tells him her roommate is going to be out of town, but the misunderstanding leads to an intimate moment for the couple. In other matters of the heart, Amy decides she's ready to have sex with Tommy (guest star Paul Wasilewski), so she works up the courage to ask Dr. Brown to write her a prescription for birth control pills, and Andy makes the important decision to talk to Ephram and Delia about Linda spending the night at their house.

Ephram is horrified and heartbroken after he impulsively tells Madison (guest-star Sarah Lancaster) that he loves her and she doesn't reciprocate. Meanwhile, Linda naively agrees to watch Delia overnight so that Andy can accompany Ephram and his piano teacher, Will (guest-star James Earl Jones), to a jazz competition in Boulder, and Amy breaks up with Tommy (guest-star Paul Wasilewski) after realizing she might not be able to trust him again.

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.

Amy moves back home, but finds adjusting to her old life difficult, especially after her parents (Tom Amandes and Merrilyn Gann) discover she's taking birth control pills and her former friends give her the major cold shoulder. Elsewhere in Everwood, Ephram thinks Madison is going to break up with him and Andy testifies on behalf of Nina as she and her recently out-of-the-closet ex-husband (guest-star Dylan Walsh) battle for sole custody of their son.

Against Andy's better judgment, ex-sweethearts Ephram and Madison decide it would be in Delia's best interest if Madison resumed her job as Delia's babysitter. Meanwhile, Amy contemplates going off her anti-depressant medication after Linda suggests she might be ready and Bright anxiously awaits his college acceptance letters.

Amy confides to Bright that she may have developed feelings for Ephram and sees him in a new light, but Bright begs her to have mercy on poor Ephram, who is still nursing a broken heart from his recent break-up with Madison. Meanwhile, Linda reveals her HIV status to Delia after the girl confronts her about all the pills she's been taking. While Delia takes the news better than expected, the rest of the town goes ballistic after Linda's secret unintentionally becomes public knowledge. Dr. Abbott faces a potential malpractice suit, and Andy is forced to come clean with Ephram, who doesn't take the news very well.

Ephram and Amy decide to go to prom together as friends, but Amy can't get up the nerve to tell Ephram that she has feelings for him after they run into his ex-girlfriend Madison and Amy realizes that he's still nursing a broken heart. Meanwhile, Linda decides it may be time to leave Everwood behind, and Andy's mentor, Dr. Donald Douglas (guest star Philip Baker Hall), asks him to perform risky brain surgery on a patient who turns out to be Dr. Douglas himself.

When Amy accompanies Ephram to his Julliard audition in Boulder, a romantic moment leads her to confess her newfound feelings for him. Meanwhile, Andy struggles to convince his mentor Dr. Douglas (guest-star Philip Baker Hall) that he needs even riskier brain surgery than originally thought and that Andy is the man to do it. Dr. Abbott faces losing his medical practice after it appears no company will insure him. Lastly, Bright decides not to attend his graduation ceremony, much to the disappointment of his family.

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.