After the death of his wife, Dr. Andrew "Andy" Brown (series star Treat Williams) trades his career as a world-renowned neurosurgeon for an opportunity to be a better parent and move his two children, 9-year-old Delia (series star Vivien Cardone) and 15-year-old Ephram (series star Gregory Smith) to Everwood, Colorado. The sudden shift is hardest on Ephram, who resents all the years his father lavished on his career at the expense of his family. When Andy opens a free medical clinic for the citizens of Everwood, people think that he is crazy, but a local woman, Edna (series star Debra Mooney), quickly applies for a job as his nurse and office manager. Edna's son, Dr. Harold Abbott, the only other doctor in town, is disturbed by the competition and forbids his children, 15-year-old Amy (series star Emily VanCamp) and 17-year-old Bright from associating with the Brown family. Traditions transform overnight for the residents of Everwood, as recounted by the school bus driver, Mr. Irv.

Andy and Ephram's fragile relationship is further strained when it appears that Andy is once again giving priority to his work instead of his family. Meanwhile, as the town of Everwood celebrates its annual Fall Thaw Festival, Ephram's interest in Amy continues to develop, and Delia gets into trouble at school for questioning her teacher's antiquated rules.

Dr. Brown's neighbor and friend Nina (recurring guest star Stephanie Niznik) is ostracized by the townspeople when they discover that she is a surrogate mother for a woman in her mid-50s. Dr. Brown's clumsy attempt to come to Nina's defense only makes the situation worse, but she turns to Dr. Brown and Ephram for help when the baby makes an unexpectedly early arrival. Meanwhile, in order to gain the approval of her friends, Amy cancels her party invitation to Ephram. And Delia tries to befriend the school bully, Magilla (Bret Loehr).

Dr. Brown and Dr. Abbott must put aside their differences 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 suspects that Bright may have been intimate with one of the patients. Meanwhile, Ephram ignores his romantic feelings in order to comfort Amy. She is distraught over not being able to go to the fall dance with her boyfriend, who has been in a coma since a car accident several months ago.

After a lost deer makes its home in the Browns' backyard, Dr. Brown insists on accompanying Ephram while he helps the animal return to the wilderness. Meanwhile, Ephram finally admits to Amy that he never asked his father to consider operating on her comatose boyfriend. Also, Delia questions the existence of God.

Amy is heartbroken--and Ephram is furious--when Dr. Brown decides against performing a risky operation on Amy's comatose boyfriend. Meanwhile, Delia is forbidden from playing with her only friend, Magilla (recurring guest star Bret Loehr), after his parents witness them playing dress-up. And a traveling psychologist, Dr. Trott (Jane Krakowski - "Ally McBeal"), creates an uproar in the Everwood community.