After the death of his wife, neurosurgeon Dr. Andrew Brown uproots his teenage son, Ephram, and 9-year old daughter, Delia, from New York to the idyllic town of Everwood, where he tries to reconnect with the emotionally distant Ephram and build a practice while competing with the town's only other physician.
Andy throws himself into his practice which puts strain on his relationship with Ephram. Delia challenges the rules imposed by her teacher and finds herself in a fistful of trouble.
Dr Brown and Ephram help deliver a neighbor's baby. Amy wins popularity with her friends by disinviting Ephram to a party. Delia tries to make friends with the school bully.
When several teens become infected with a sexually transmitted disease, Dr. Brown and Dr. Abbott work together to treat the town and to educate the townspeople.
When a doe takes up residence in the Brown’s backyard, Ephram decides to lead it back to the wild. Andy insists on joining him and the two city slickers set out to conquer the wilderness. Meanwhile, Delia questions God after a classmate tells her that he doesn’t exist.
Andy doubts his abilities and refuses to operate on Amy's comatose boyfriend. Delia is forbidden from playing with her friend after his parents discover the two of them playing dress up.
Dr. Brown performs a risky surgical procedure on Amy's boyfriend.
As his wedding anniversary approaches, Andy fears that he will never feel complete again. Ephram kisses Amy on a school field trip. Mrs. Abbott forces her husband to join her for salsa lessons.
Ephram and Delia's grandparents Jacob and Noni arrive unannounced and begin to overwhelm Andy and critique his parenting skills. Ephram finds a stronger bond with Jacob than with his father. Noni competes with Edna for Delia's love.
Jacob and Noni throw a party for Edna. As a snowstorm hits, Bright's appendix bursts and Andy is called upon to perform an emergency surgery, while he and Ephram air their grievances against one another.
Ephram tries his best to revive his mother's Thanksgiving traditions. Meanwhile, Andy tries to save a patient's life by finding his missing brother.
A heartbroken Ephram watches as Amy readies for Colin's return home. Andy and Dr. Abbott consider the debate over medical marijuana.
Ephram is offered the lead in Everwood's production of "The King and I", but is emotionally torn when Amy's boyfriend Colin wants to be friends with him.
Andy tries to coax Ephram into playing the piano again. Nina's estranged husband comes back to Everwood.
Amy and Colin kiss during the church ski trip, as Ephram finds himself intrigued with Colin's younger sister. Meanwhile, Andy begrudgingly attends a singles mixer.
When Dr. Gretchen Trott comes back to town, Andy must face up to his romantic feelings for her. Meanwhile, Ephram asks Laynie out on a first date.
Dr. Abbott's father is implicated in a murder that took place 30 years ago, leading Dr. Abbott and Andy to figure out the truth. Ephram's recurring thoughts about Amy cause difficulties for his new relationship with Laynie.
Ephram confronts a past infidelity on his father's part as the anniversary of his mother death approaches. Amy begins to worry that Colin hasn't healed properly from his surgery when he gets sick during the course of their date.
While Amy and Bright downplay the troubles of Colin's recovery, Ephram becomes convinced of their existence when he witnesses Colin trashing the gym teacher's office. Meanwhile, a New York reporter is curious about why Dr. Brown still lives in Everwood, and Delia decides to try and hide out in the Museum of History for a night while on a class trip.
Ephram prepares to play his first piano recital in Everwood. Drs. Brown and Abbott attempt to determine the cause of a man's bruise-inducing sleep disorder. Meanwhile, Amy's feigned interest in spending time with her grandmother allows her to stay close to Colin, and Everwood is talking UFOs following the sighting of mysterious lights in the sky.
Dr. Brown is at a moral crossroads when a young girl and her father come to him for counsel about ending her pregnancy. Meanwhile, Ephram's Spring Formal date leaves him during the dance in order to go off with her boyfriend, prompting Amy and Colin to fight over her decision to subsequently console Ephram.
When Ephram is forced to go with Andy and Irv to a lakeside cabin, he decides to take a boat out by himself despite a lack of boating experience and ends up in a serious accident. Meanwhile, Colin and his parents consider whether or not Colin should undergo a risky second surgery, and Nina confronts her cheating husband.
As Colin's surgery date draws closer, Andy takes Ephram and Delia on a road trip to consult with his old medical school mentor. Meanwhile, Colin abducts Amy and Bright in the middle of the night in hopes of spending the day recounting some fond memories and looking ahead.