After their house has been sold, Nina and Sam temporarily move in with the Browns. Wanting to take care of an unresolved issue in his life before he can propose to Nina, Andy takes a mysterious trip. Bright learns that Hannah has received a scholarship to Notre Dame and is devastated at the thought that she may accept it. Edna upsets Harold and Rose when she reveals her plans to leave Everwood. Delia is thrilled with Andy’s belated Bat Mitzvah gift.

Dr. Brown and Dr. Abbott must put their striking differences aside 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 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 who remains in a coma.

Andy's neighbor and friend Nina (Stephanie Niznik) 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 disinvites him to a party in order to gain the approval of her friends; and Delia attempts to befriend the school bully, Magilla (guest star Bret Loehr).

After his wife is killed in a car accident, Dr. Andrew Brown moves his 15-year-old son, Ephram, and 9-year-old daughter, Delia, to the idyllic environs of Everwood to make a new start. In the opener, the relocation sparks harsh words and hurt feelings between the emotionally distant father and his neglected son, despite Andrew's attempts to reconnect with the teen. The good doctor also runs afoul of the town's only other physician when he decides to open his own practice---right across the street from his rival's office.

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.

Andy meets with Colin's parents to discuss a potential course of treatment for the comatose teen. 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 (guest star Bret Loehr), after his parents discover them playing dress up. Dr. Trott, a traveling psychologist (guest star Jane Krakowski) sets up shop and stirs up the emotions of several townspeople who seek her guidance, much to the chagrin of a distrustful Dr. Abbott.

As the day of Colin's (guest star Mike Erwin) surgery approaches and emotions run high, Andy takes Ephram and Delia on a road trip to his old medical school to consult with his mentor, Dr. Donald Douglas (guest star Philip Baker Hall). Back in Everwood, Colin kidnaps Amy and Bright in the middle of the night to surprise them with a special day of memories and hopes for the future.

The former Big Apple neurosurgeon, Dr.Andrew Brown, puts on his scrubs for the first time since he relocated his family to Colorado to operate on Amy's comatose boyfriend, Colin (Mike Erwin), with the help of his friend and surgery partner from New York, Dr. Brian Holderman (guest star Lamont Thompson). Adding to his performance anxiety is the identity of the patient---Colin Hart, the boy who was dating Amy before she stole Ephram's heart. It also doesn't help that the tricky procedure he plans to perform has never been attempted before. 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 Colin's former life in Everwood is also revisited as flashbacks reveal some startling secrets about the teen's last days before the accident that put him in the hospital.

Dr. Abbott suspects that Linda and Andy like each other more than they should, so he decides to set his sister up with more appropriate suitors. Meanwhile, Ephram finally has the courage to tell Amy how he really feels about their relationship, but he is confused by his feelings for Madison, who comes to the rescue when Ephram needs help to pass his driving test. Meanwhile, Andy tries to help the soon-to-be-remarried Reverend Keyes (guest-star Tim DeKay) cope with his impending blindness, but the minister would rather leave his fate to God than attempt a new treatment that might save his sight.

Dr. Brown faces one of the toughest moral decisions of his career when a distraught pregnant teenager (guest star Kate Mara) and her father (guest star Kevin Tighe) come to him for guidance about terminating her pregnancy. Meanwhile, Ephram is humiliated in front of the entire school when his date for the Spring Formal ditches him at the dance to make-out with her boyfriend. Lastly, Amy and Colin (Mike Erwin) have a huge fight when she chooses to console Ephram against Colin's wishes.

Ephram reveals information about his dad to Nina that surprises her and adds a new twist to her inner Andy-or-Jake struggle; Andy finds more of a connection with his dad (guest star Charles Durning), who's still in town; Amy and Ephram recall a moment from their past that helps Amy realize that Ephram is always there for her. Lastly, Hannah and Bright come together as friends, realizing that there's still a close bond between them.

Ephram prepares to leave for Europe as he feels that he has nothing left for him in Everwood. However, he's caught off-guard and questions his plans when Andy reveals the secret that Amy has been keeping from Ephram. Meanwhile, Nina and Jake contemplate going into business together, but the stress on their relationship proves a big obstacle to overcome. Meanwhile, Bright finally confesses he has feelings for Hannah.

Dr. Brown courts Linda Abbott despite Edna's and Harold's insistence that he's wasting his time, but Andy persists, forcing Linda to tell him that she is H.I.V. positive. Bright tells Ephram he can win Madison's affections by ignoring her, but the plan goes awry when she breaks up with her boyfriend. Amy meets a flirtatious and attractive town bad-boy, Tommy Callahan (guest star Paul Wasilewski), whose compassion for her problems touches her heart for the first time since Colin's death.

After a lost deer makes the Brown's backyard its new home, Andy insists on accompanying Ephram who decides to help the animal find its way home to the wilderness, where the journey includes a long hike through the mountains. Meanwhile, Ephram finally admits to Amy that he never asked his father to consider operating on her boyfriend, Colin, who is in a coma. Lastly, Delia questions the existence of God after a classmate tells hear that he doesn't believe in higher beings.

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.

Amy and Ephram decide to meet at the Abbotts' Cabin to take their relationship to the next step as both parents on each side worry as they know their kids intentions. Although while there they realize they may not be able to handle it. Andy and Amanda chaperone Delia and Charlie on a date. Although the evening turns when Andy and Amanda begin to feel they are on a date. Lastly, Nina turns to Jake when Sam is hurt while ice skating and her feelings for him change.

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.

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. Although Bright tells Ephram that Amy is using him just go get his father to get Colin out of coma. Delia gets into trouble at school for questioning her teacher's antiquated rules.

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.

With Ephram (Gregory Smith, who does not appear in the episode) gone and no longer feeling any significant ties to Everwood, Andy consults with Delia and contemplates accepting a prestigious position with a Chicago hospital. Uncharacteristically upset over this bit of news, Harold takes it upon himself to give Andy a reason to stay. Meanwhile, Jake moves in with Nina, causing Andy to question whether he should rock the boat by telling her how he really feels, and Bright finally admits his feelings to Hannah.

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.

On a church ski trip chaperoned by perpetual party pooper Dr. Abbott, Amy and Colin share their first kiss since the surgery. Ephram finds himself intrigued by Colin's younger sister, Laynie (guest star Nora Zehetner), who has recently returned home from boarding school. Also, Bright attempts to get to the next base with his girlfriend (guest star Devon Reilly). Meanwhile, Andy hesitantly agrees to attend a singles mixer with the recently divorced Reverend Keyes (guest star Tim Dekay).

While packing up her house and preparing to leave Everwood with Jake, Nina tells Hannah that she knows Andy bought an engagement ring for her. Hannah convinces Nina to sneak into the house while the Browns are out to get a look at the ring. Later, Jake finds out about the ring and confronts Andy once again about his feelings for Nina. At Delia’s Bat Mitzvah, Amy watches Ephram with his new girlfriend Stephanie, and realizes her feelings for Ephram are still strong. When one of Harold’s patients leaves her baby on the Abbott’s doorstep, Harold wrestles with the right course of action while Rose immediately becomes attached to the little girl.

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.

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(Merrilyn Gann) proposes they take salsa dancing lessons. Andy also helps a couple whose marriage problems are caused by hives.

Just out of the hospital and wanting to start his life over, Reid asks Amy out on a date. Amy talks a very reluctant Hannah into a double date with Amy's friend Nick, leaving Bright to deal with his pain and jealousy. Delia panics when her Bat Mitzvah falls on the same day as the birthday party of the most popular girl at school. Nina tries to deal with her confusing emotions over Andy and realizes she will have to make a decision when Jake asks her to move to Los Angeles with him. Harold points out to Rose that they were so caught up in the adoption procedure they've been taking each other for granted.

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.

Andy and Jake are in therapy together with a councillor as they have some issues to settle. Nina leaves them to debate.

Amanda decides to send her husband to a very nice treatment facility causing Andy to collapse as a result of stress and guilt over what has happened between him and Amanda. Meanwhile, Amy continues to give Ephram the cold shoulder for lying about Madison, Also Edna builds a writing room for Irv.

When Jake's girlfriend (guest-star Jessica Collins) from Los Angeles arrives in Everwood unexpectedly, Nina comes to his rescue with a shoulder to lean on as he wants to get rid of her and the possibility of more with Nina. Also, Ephram and Amy are back together. He is being the "new supportive boyfriend she deserves." Meanwhile, Harold and Rose worry about Amy after she sets her mind to auditioning for a rigorous ballet program in Denver, and Andy unintentionally humiliates Delia in front of her hockey team.

An angry Ephram makes a bold move - and breaks his father's heart in the process - in an attempt to raise money for a plane ticket to Europe by selling his music equipment, except his piano, to "muscian" Jared and his band. Meanwhile, Nina can't quite put her finger on why Andy has been acting strangely of late, whereas a more perceptive Delia comes right out and asks her father whether he has feelings for Nina, and Bright's green-eyed monster makes an unexpected appearance when Hannah (Sarah Drew) goes to the prom with Topher (guest-star Lukas Behnken). Hannah becomes very upset when Bright insults her dress. Bright goes apartment hunting. Lastly, Rose begins her treatment at the hospital with Harold by her side.

Ephram and Amy are reunited after a long summer spent apart while Ephram attended Julliard's summer program in New York, but Amy's euphoria is quickly replaced with paranoia after she notices Ephram acting distant. Meanwhile, Andy is plagued by guilt over whether he made the right decision concerning Madison's pregnancy, and Dr. Abbott befriends the town's newest citizen, Jake Hartman, who turns out to be a doctor from California looking to open a new practice in Everwood.

An eighteen-year-old girl wants Andy to check her for the breast cancer gene, as it runs in her family. The girl and her older sister (who already had cancer and a double mastectomy) go see Andy for the results. Bright and Hannah are out on a date when something happens to both of them, and they call Harold. Kyle doesn't want lessons from Ephram anymore, again.

Andy and Amanda (guest-star Anne Heche) decide that it's time to tell Delia and Charlie (guest-star Shane Haboucha) about their relationship before they hear about it elsewhere, but Charlie's emotional reaction makes them question what they're doing. Meanwhile, when Hannah (Sarah Drew) doesn't jump at the opportunity to go on a date with a really cute guy, Topher, from school, Amy is convinced that Hannah is misguidedly saving herself for Bright. Nina questions whether Sam (guest-star Jimmy Bennett) is going to be hurt again if her relationship with Jake (Scott Wolf) doesn't work out. Lastly, we flashback to Amanda (Anne Heche) and John earlier in their marriage of a more happier time with their son Charlie, right before he has his stroke.

When traveling psychologist Dr. Gretchen Trott (guest star Jane Krakowski) comes back into town, Andy is forced to confront his potentially romantic feelings for her. In other romantic entanglements, Edna and Irv have difficulty adjusting to life after his heart attack scare; Harold and his wife Rose (guest star Merrilyn Gann) have it out after they attend couples therapy and she suggests that he's lost that lovin' feeling; and Ephram asks Laynie (guest star Nora Zehetner) out on their first date, in part to show Amy that he's moving on with his life.

As Andy finally realizes that his feelings for Amanda (Anne Heche) are only growing stronger despite his best efforts to maintain a platonic friendship, Andy decides it's in both of their best interests if he refers her husband's case to Dr. Abbott from now on. Upon hearing news that Madison (Sarah Lancaster, who does not appear in the episode) and her band are performing in Everwood, Ephram seeks guidance from Bright, signalling a thaw in the boys' chilly relationship as of late with Ephram and Amy dating. Lastly, Amy's curiosity brings about Hannah's (Sarah Drew) family secret.

Horrified to discover that Ephram and Madison are involved, Dr. Brown stops short of firing her, but Madison decides to quit leaving the Browns to a very unhappy holiday, especially when Delia discovers another troubling relationship - between her father and Linda Abbott. Stressed by Thanksgiving with his cantankerous mother-in-law (guest star Betty White), Dr. Abbott reacts badly when Amy brings Tommy (Paul Wasilewski) to Thanksgiving dinner. Finally pushed to the breaking point, Amy runs away from home.

As if adjusting to college life and the news that her secret crush, Reid (guest star Justin Baldoni), is gay weren't enough to handle, Amy learns that Ephram is going to be a regular fixture in her life now that he's moved in with Bright and Reid. Meanwhile, Andy, Nina and Jake attempt to move on with life after Nina decides which man she loves---which is Jake. Bright and Ephram take Hannah to a college party. Andy gets involved in a case dealing with 17-year old Ethan Harcourt who is on anti-depressants since his older brother's car accident and death, but now wants to be intimate with his current girlfriend. Although, the anti-depressants he is taking is causing erectile dysfunction for him and tries to coerce Andy in letting him have Viagra. Ethan wants to keep all of this a secret from his girlfriend and family who don't know about his situation. Andy wavers that he's too young but Ethan doesn't listen and purchases medication online that inevitably ends him up in the hospital after

Ephram is horrified and heartbroken after he impulsively tells Madison (guest-star Sarah Lancaster) that he loves her and she doesn't reciprocate. Meanwhile, Linda naively agrees to watch Delia overnight so that Andy can accompany Ephram and his piano teacher, Will (guest-star James Earl Jones), to a jazz competition in Boulder, and Amy breaks up with Tommy (guest-star Paul Wasilewski) after realizing she might not be able to trust him again.

Amy moves back home, but finds adjusting to her old life difficult, especially after her parents (Tom Amandes and Merrilyn Gann) discover she's taking birth control pills and her former friends give her the major cold shoulder. Elsewhere in Everwood, Ephram thinks Madison is going to break up with him and Andy testifies on behalf of Nina as she and her recently out-of-the-closet ex-husband (guest-star Dylan Walsh) battle for sole custody of their son.

Hannah's mother (guest star Jayne Brook, "Chicago Hope") pays an unexpected visit to Everwood to tell Hannah that her father has passed away. Elsewhere in Everwood, Ephram stifles his feelings for Amy while forced to watch her relationship with Reid (guest star Justin Baldoni) grow more serious; Andy advises a patient (guest star Keith David, "Crash") who desperately needs a kidney transplant, but refuses to accept one from his daughter (guest star Gina Ravera). Lastly, Bright is at a loss at how best to help Hannah through this difficult time.

Ephram gets the wrong idea when Madison tells him her roommate is going to be out of town, but the misunderstanding leads to an intimate moment for the couple. In other matters of the heart, Amy decides she's ready to have sex with Tommy (guest star Paul Wasilewski), so she works up the courage to ask Dr. Brown to write her a prescription for birth control pills, and Andy makes the important decision to talk to Ephram and Delia about Linda spending the night at their house.

Andy manages to get tickets for a piano concert he and Ephram attend. After, Ephram and the pianist talk about playing professionally. Bright meets a girl from his past again, which makes him think about his current relationship with Hannah.

Andy finds himself at a loss over what to do when Delia naively stumbles upon Nina's vibrator and starts asking questions. Meanwhile, Ephram attempts to write Amy a love letter to show her the extent of his feelings. Amy makes it her mission to make new best friend Hannah (Sarah Drew) popular. Meanwhile, Harold and Rose question Bright's euphoria over being selected "employee of the month" and decide it's time for some parental intervention. Dr. Abbott becomes worried that his son Bright is settling too little in life when taking a job at a restaurant. Lastly, Andy treats a patient who needs a transplant, but won't tell his wife.

Bright takes Ephram to one of the college keggers to help cheer him up for some reason, but Ephram ignores the girls who are flirting with him and the party as he's playing video games. Also, lonely Edna suffers a panic attack and is rushed to the hospital. Lastly, Delia grows more rebellious against her father. Harold and Rose consider adopting a child from Africa, but the process of it is a lot harder than they expected.

Ephram seeks guidance from his and piano mentor, Will Cleveland (guest-star James Earl Jones) when he's struggling to select the music program for his Julliard audition tape. Things don't go well for Ephram as he faces losing one of the most important relationships in his life after he accidentally hurts Will's feelings. Meanwhile, Bright takes a job working at the restaurant, "The Firehouse" where he meets waitress Serena. Things go bad though when they get caught by their boss in the most compromising position in the closet. Lastly, Andy and Amanda experience a miraculous breakthrough in their music therapy with Amanda's husband (guest-star Jason Beghe), but Andy quickly questions the results.

When Andy's relationship with Delia is threatened after he breaks his promise not to date Linda Abbott, he decides to take his daughter on a special bonding trip to regain her trust. Andy is also surprised by Ephram's emotional reaction to the relationship with Linda. Meanwhile, Andy finds himself in a tough spot when a woman patient wants to get pregnant through in-vitro fertilization with sperm from her first husband, who is now dead, but her second husband is having a real problem over the matter. The Abbott family is still in turmoil when Amy decides to live with Edna and Irv, rather than playing by her parents' rules.

Andy consults Josh Stein, who's studying to become a rabbi. Josh also helps Delia with her Bat Mitzvah. Ephram supports Kyle, as his father comes to town. Amy's professor talks to Harold about a medical procedure. Andy is trying to go on a date with someone he met over the internet, but he has to postpone multiple times.

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.

Ephram regrets promising Nina that he would watch over Hannah at school, especially when her constant presence interferes with his time alone with Amy. Amy befriends Hannah out of a sense of charity, but soon finds Hannah so refreshing that a real friendship develops. Meanwhile, Andy tries to ignore the tension between Dr. Abbott and Edna, but his attitude forces Edna to quit and go to work for Dr. Hartman. Andy treats a 13-year-old patient (guest-star Carter Jenkins) whose mysterious injuries cause Andy to suspect the boy's mother (guest-star Elizabeth Mitchell) of abuse.

Just as they've become somewhat comfortable with their new relationship, Andy and Amanda receive word that Amanda's husband, John (guest star Jason Beghe), has experienced a miraculous breakthrough in his recovery. Meanwhile, Amy learns the truth about why Madison really left town, an elated Ephram is offered an audition at Julliard, Hannah questions whether she's emotionally prepared to take the test for Huntington's Disease, and Bright is accused of sexual misconduct in the workplace.

Ephram discovers that Bright cheated on Hannah and confronts him about it. Irv takes Edna along on his book tour, where they meet his daughter Cassie. Reid is faced with expulsion from medical school for cheating on an exam. Harold confesses to Andy that he neglected to report Rose's cancer on the adoption application. Ephram tells Amy what happened with Bright, prompting her to confront him and force him to admit the truth to Hannah.

The entire Abbot's family is turned upside down by the return of Dr. Linda Abbott (Marcia Cross, ""Melrose Place""), who has been practicing Eastern-based medicine in exotic locations around the world. Edna, who is blinded with pride, doesn't see her daughter's loneliness, and loses sight of her own life with Irv. But Linda encounters the most resistance from her brother Harold when she announces her decision to join his practice. Meanwhile Andy learns that some 'tweens may be practicing unsafe sex, and is shocked at their parents reaction to the situation. Finally, Bright asks Ephram to keep an eye on Amy whose odd behavior has everyone worried.

Ephram rescues Reid from attempted suicide as Reid suffers depression from finding out that he has been kicked out of Med School. Nina confesses to Andy that she still shares feelings for him. A necklace is passed between Harold and Bright as each try to apologize to Rose and Hannah.