Although conflicted by his feelings for Amy, Ephram finds himself serving as confidante and friend to Amy's boyfriend, Colin, who continues to feel like a fish-out-of-water as he attempts to reclaim his life before the accident. Meanwhile, Andy hopes to convince Ephram to resume the piano lessons he abandoned after his mother's death; Nina's absentee husband (guest star Dylan Walsh) comes home for a visit, which proves to be far from happily ever after; and in a bittersweet turn of events, Amy and Colin are nominated for Homecoming King and Queen.

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.

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.