Dr. Brown and Dr. Abbott must put their striking differences aside to educate the town of Everwood after several of their teenaged patients are diagnosed with a sexually transmitted disease. To make sensitive matters worse, Dr. Abbott has reason to suspect that his son, Bright, may have been intimate with one of the patients. Meanwhile, Ephram pushes his romantic feelings aside to comfort Amy who is distraught over not being able to go to the Fall Dance with her boyfriend who remains in a coma.

As his wedding anniversary draws near, Andy loses all hope and questions whether he will ever feel his life is worth living again. Meanwhile, Ephram and Amy share their first kiss while on a field trip; and Dr. Abbott has a panic attack when his wife Rose(Merrilyn Gann) proposes they take salsa dancing lessons. Andy also helps a couple whose marriage problems are caused by hives.

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.

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.

A nervous Ephram feels the pressure of performing his first piano recital in Everwood; Dr. Brown and Dr. Abbott attempt to diagnose a man (guest star Dan Merket) with a mysterious sleeping disorder that leaves welts on his body; and Amy pretends to want to spend time with her grandmother, Edna, in order to secretly see Colin while she's grounded. Meanwhile, the town is buzzing with rumors of UFOs and aliens after locals observe something strange in the sky.

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.

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 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.

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.

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 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 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.

Ephram regrets promising Nina that he would watch over Hannah at school, especially when her constant presence interferes with his time alone with Amy. Amy befriends Hannah out of a sense of charity, but soon finds Hannah so refreshing that a real friendship develops. Meanwhile, Andy tries to ignore the tension between Dr. Abbott and Edna, but his attitude forces Edna to quit and go to work for Dr. Hartman. Andy treats a 13-year-old patient (guest-star Carter Jenkins) whose mysterious injuries cause Andy to suspect the boy's mother (guest-star Elizabeth Mitchell) of abuse.

Andy puts his foot in his mouth by picking a fight with Everwood's patron saint, Amanda Hayes (Anne Heche), who, unbeknownst to Andy, has been caring for her profoundly disabled husband (guest-star Jason Beghe) for the past five years. Meanwhile, Jake surprises Nina by asking her out on a date; Ephram and Bright realize their friendship may have grown too far apart to salvage; and neurotic-as-ever Dr. Abbott struggles to come up with a medical invention after learning that Dr. Brown and Dr. Hartman have successful inventions of their own.

Feeling conflicted over the recent turn of events and not willing to jeopardize Ephram's Julliard audition, an angst-filled Amy tells Ephram that he should take Andy to New York instead of her. In New York, Andy struggles with memories of his former life and the desire to tell Ephram the truth about Madison. Fate plays a hand when Ephram runs into Madison in Manhattan and they make plans to see each other, causing Andy to take matters into his own hands. The episode was partially filmed in New York City.

After returning from New York feeling lost and confused and needing Amy for support, Ephram considers his options in the wake of Madison's (Sarah Lancaster, who does not appear in this episode) life-altering revelation. Ephram tries to find the baby by going to Child Services Office, but finds out that Madison signed the adoption papers with "father unknown" and terminating the parent-child relationship with "Unknown Birth Father" leaving Ephram completely crushed.

Amy tries to get Ephram another audition at Julliard after he missed his first appointment due to the emergency with Madison and the baby, but it doesn't go well. Meanwhile, a tired Andy is a little stunned upon learning the extent of Nina's feelings for Jake and with a little encouragement from her friend Bright, Hannah decides to go on a date with a smitten Topher (guest-star Lukas Behnken).