Although Amy and Bright are still living in denial regarding the state of Colin's (Mike Erwin) recovery, Ephram can't ignore the bad signs any longer after he witnesses Colin freaking out and vandalizing the gym teacher's office. Meanwhile, a New York Magazine reporter pays a visit to Dr. Brown in hopes of uncovering the truth behind why the famed surgeon is still living in Everwood. And Delia decides to secretly spend the night in the Museum of History while on a school field trip.

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.

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.

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.