Dr. Andrew Brown is a world-famous neurosurgeon whose career always overshadowed his obligations as a parent, until the day that his loving wife died. Faced with the daunting task of raising his two kids, 9-year-old Delia and 15-year-old Ephram by himself, Andrew moves his family from New York to the beautiful Rocky Mountain town of Everwood, Colorado, where he opens a free medical clinic. Delia adjusts quickly to her new surroundings, but the sudden shift in everything he has ever known is hardest on Ephram, who resents all the years his father lavished on his career...
Andy and Ephram's fragile relationship is further strained when it appears that Andy is once again putting work before family. Meanwhile, as the town of Everwood celebrates its annual Fall Thaw Festival, Ephram's interest in Amy continues to blossom and Delia gets into trouble at school for questioning her teacher's antiquated rules.
Andy's neighbor and friend Nina is ostracized by the townspeople when they discover she is a surrogate mother for a woman in her mid-50s. Andy's clumsy attempt to come to Nina's defense backfires, but she turns to him and Ephram for help when the baby makes an unexpectedly early arrival. Meanwhile, Ephram is dealt an emotional blow when Amy dis-invites him to a party in order to gain the approval of her friends, and Delia attempts to befriend the school bully, Magilla.
Dr. Brown and Dr. Abbott must put their striking differences aside to educate the town of Everwood after several of their teen-aged 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, as he is still comatose.
After a lost deer makes the Browns' backyard its new home, Andy insists on accompanying Ephram, who decides to help the animal find its way home to the wilderness. Meanwhile, Ephram finally admits to Amy that he never asked his father to consider operating on her boyfriend, Colin, who is in a coma; and Delia questions the existence of God.
Amy is heartbroken and Ephram is furious when Andy decides against performing a risky operation on Amy's comatose boyfriend. Meanwhile, Delia is forbidden from playing with her only friend, Magilla, after his parents discover them playing dress up; and a traveling psychologist, Dr. Trott, creates quite a stir in the Everwood community.
As Dr. Brown operates on Amy's comatose boyfriend Colin with the help of his friend and surgery partner from New York, Dr. Brian Holderman, Amy leans on Ephram for support as she awaits the outcome. Meanwhile, an emotional Bright breaks down and admits what actually happened the day of the car accident.
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 proposes they take salsa dancing lessons.
Andy's parenting skills are questioned when Ephram and Delia's grandparents pay them an unexpected visit to check up on their son-in-law. Meanwhile, Ephram sneaks out of the house to see Amy who is still emotionally recovering from the aftermath of Colin's surgery.
Delia and her grandmother throw a festive birthday party for a grumpy Edna who hates this particular day of the year, but everyone winds up snowed in for the night when a big storm hits town. In the midst of it all, Bright collapses from a burst appendix and Andy and Dr. Abbott have to improvise an operating room before the infection spreads; while Andy and Ephram let months of tension and hurt feelings explode in front of everyone with a threat of Ephram moving back to New York with his grandparents.
In hopes of raising his little sister Delia's spirits, Ephram does his best to recreate his mother's Thanksgiving traditions as the Brown family spends their first holiday without her. Meanwhile, in order to save a patient's life, Dr. Brown must find the man's missing brother, who is believed to live in the woods; and curmudgeonly Dr. Abbott attempts to befriend the entire town when he has a health scare and questions whether anyone would attend his funeral.