In last season's emotional cliffhanger, Dr. Brown performed radical brain surgery on Colin Hart in an effort to save his life. In the series' dramatic second season premiere, Colin's fate will be revealed.
Andy is concerned that Ephram needs more extracurricular activities to get into a top college, but Ephram is only focused on his Juilliard 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 with ruptured breast implants, who cares more about looking good than her own health.
The entire Abbot family is turned upside down by the return of Dr. Linda Abbott, who has been practicing Eastern-based medicine in exotic locations the world. Edna, who is blinded with pride, doesn't see her daughter's loneliness, and loses sight of her own life with Irv. But Linda encounters the most resistance from her brother Harold when she announces her decision to join his practice. Meanwhile, Andy learns that some 'tweens may be practicing unsafe sex, and is shocked at their parents reaction to the situation. Finally, Bright asks Ephram to keep an eye on Amy, ...
Andy's well-intentioned plan to give Ephram more free time by hiring college student Madison Kellner 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 blinds him to Nina's struggles with her divorce proceedings. Dr. Abbot continues to clash with his sister, Linda, when she tries to take over his office and the difference in their personalities and medical philosophies become alarmingly clear.
When Andy invites Linda 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. 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. Andy tries to help the soon-to-be-remarried Reverend Keyes 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, along with Edna, Linda, and Harold, rush to the scene to assist their neighbors. One miner is Will Cleveland, a jazz pianist who has recently become Ephram's mentor; another is Abbott's next door neighbor, whose outrageous building plans Harold has tried to thwart; and the third Andy's patient Ellie Beels, 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 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 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 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, 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, Andy 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. Stressed by Thanksgiving with his cantankerous mother-in-law, Dr. Abbott reacts badly when Amy brings Tommy 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, 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. 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 puts his life in jeopardy for an important tournament. Bright is suspended from school after he fights with Amy's boyfriend Tommy. Linda 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, 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, 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 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, to a jazz competition in Boulder, and Amy breaks up with Tommy after realizing she might not be able to trust him again.
When Ephram gets a fake I.D. so that he can get into a bar to see Madison's band, he ends up in a bar fight and Andy has to bail him out of jail. 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. Finally, Tommy takes Amy to a party where she finds closure over the loss of Colin, but the evening takes a life-threatening turn.
Amy moves back home, but finds adjusting to her old life difficult, especially after her parents 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 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, 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, when Linda's HIV status is accidentally revealed to her patients, 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 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, 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 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; and 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.