On a church ski trip chaperoned by perpetual party pooper Dr. Abbott, Amy and Colin share their first kiss since the surgery. Ephram finds himself intrigued by Colin's younger sister, Laynie (guest star Nora Zehetner), who has recently returned home from boarding school. Also, Bright attempts to get to the next base with his girlfriend (guest star Devon Reilly). Meanwhile, Andy hesitantly agrees to attend a singles mixer with the recently divorced Reverend Keyes (guest star Tim Dekay).

When traveling psychologist Dr. Gretchen Trott (guest star Jane Krakowski) comes back into town, Andy is forced to confront his potentially romantic feelings for her. In other romantic entanglements, Edna and Irv have difficulty adjusting to life after his heart attack scare; Harold and his wife Rose (guest star Merrilyn Gann) have it out after they attend couples therapy and she suggests that he's lost that lovin' feeling; and Ephram asks Laynie (guest star Nora Zehetner) out on their first date, in part to show Amy that he's moving on with his life.

When Dr. Abbott's dementia-plagued, elderly godfather (guest star Luke Askew) confesses to a murder that took place 30 years ago and reveals that Abbott's father was his accomplice, Abbott and Dr. Brown join the investigation in an attempt to find out what really happened and clear the men's names. Meanwhile, Ephram can't seem to keep Amy (Emily VanCamp) far from his thoughts, causing major problems in his burgeoning relationship with Laynie (Nora Zehetner). Dr. Brown butts heads with Ephram's new piano teacher (guest star Ian Vogt) over what is best for Ephram.

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.

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.

The entire Abbot's family is turned upside down by the return of Dr. Linda Abbott (Marcia Cross, ""Melrose Place""), who has been practicing Eastern-based medicine in exotic locations around 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 whose odd behavior has everyone worried.

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.

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.

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.