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.

A very-much-in-love Ephram discovers that he has unwittingly become a "girlfriend" to Amy, but the friendship takes a turn for something more when a moment of intimacy leads to them waking up together the next morning. Meanwhile, Nina grows suspicious of Jake's recent strange behavior, which is further amplified when his brother, Brian (guest star Tom Parker), shows up unexpectedly. Delia takes up with the popular girls in school, which worries Andy. Also, Bright tries to rectify Hannah's low self-esteem issues. Lastly, Rose drops some startling news on Harold, which could drastically change their lives.

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.

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.

Nina finds Andy and Amanda (Anne Heche) together causing her to question Andy and her friendship with him. Meanwhile, Ephram and Amy convince a reluctant Hannah to ditch school for the day and take Bright along for the ride as the recover from sending out college applications. Lastly, Harold and Edna are forced to work together despite their hostility toward each other when a medical emergency comes up at his office with the water pipes bursting.

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.

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.

Ephram and Amy decide to go to prom together as friends, but Amy can't get up the nerve to tell Ephram that she has feelings for him after they run into his ex-girlfriend Madison and Amy realizes that he's still nursing a broken heart. Meanwhile, Linda decides it may be time to leave Everwood behind, and Andy's mentor, Dr. Donald Douglas (guest star Philip Baker Hall), asks him to perform risky brain surgery on a patient who turns out to be Dr. Douglas himself.

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.

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.

When Amy accompanies Ephram to his Julliard audition in Boulder, a romantic moment leads her to confess her newfound feelings for him. Meanwhile, Andy struggles to convince his mentor Dr. Douglas (guest-star Philip Baker Hall) that he needs even riskier brain surgery than originally thought and that Andy is the man to do it. Dr. Abbott faces losing his medical practice after it appears no company will insure him. Lastly, Bright decides not to attend his graduation ceremony, much to the disappointment of his family.

Ephram is on cloud nine after being accepted into Julliard's summer program, but his emotions are sent into a tailspin when Amy shares her feelings for him and asks that he stay in Everwood for the summer. Meanwhile, Dr. Abbott's family thinks he's gone off the deep end when he decides to open a bagel shop in response to losing his malpractice insurance, and Andy learns a shocking revelation about his family.

Andy learns that Ephram has no intention of moving back home, while Bright invites Ephram to move in with him and Reid (Justin Baldoni). Meanwhile, Hannah (Sarah Drew) begins to worry about the long term possibilities for her relationship with Bright after he shares his "three dates and out" policy; Harold suspects Andy is up to something after he frequently goes missing from the office. Nina and Jake have the grand opening for their new restaurant, Sam's. Nina is having a hard time convincing Everwood patrons on her new restaurant politics as "Mama Joys" is officially gone. But Nina gets some help when a couple of celebrities walk in and like her new establishment. Lastly, Ephram and Amy finally confront the unspoken fate of their relationship.

With Hannah leaving for Minnesota in a few days with her mother (guest star Jayne Brook, "Chicago Hope"), Bright and Amy find themselves taking the loss of their girlfriend and best friend, respectively, harder than even they expected. Jake sets out on a high-risk bike trip with his friend, Cliff (guest star Simon Rex), that takes a near fatal turn; Andy and Harold uncharacteristically decide to go skydiving after hearing of Jake's daredevil ways; and Reid (guest star Justin Baldoni) keeps his promise to Ephram and backs off from pursuing Amy, leaving her feeling all the more lonely.

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.

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.

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.

Amy confides to Bright that she may have developed feelings for Ephram and sees him in a new light, but Bright begs her to have mercy on poor Ephram, who is still nursing a broken heart from his recent break-up with Madison. Meanwhile, Linda reveals her HIV status to Delia after the girl confronts her about all the pills she's been taking. While Delia takes the news better than expected, the rest of the town goes ballistic after Linda's secret unintentionally becomes public knowledge. Dr. Abbott faces a potential malpractice suit, and Andy is forced to come clean with Ephram, who doesn't take the news very well.

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.

Andy puts his foot in his mouth by picking a fight with Everwood's patron saint, Amanda Hayes (Anne Heche), who, unbeknownst to Andy, has been caring for her profoundly disabled husband (guest-star Jason Beghe) for the past five years. Meanwhile, Jake surprises Nina by asking her out on a date; Ephram and Bright realize their friendship may have grown too far apart to salvage; and neurotic-as-ever Dr. Abbott struggles to come up with a medical invention after learning that Dr. Brown and Dr. Hartman have successful inventions of their own.

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 is back in town and is giving piano lessons at ECC now. Ephram begins his piano tutor session with a 13 year-old Kyle Hunter who has a major attitude. He doesn't want to play the "classical crap" though. He wants to go to Julliard, which Ephram finds funny but isn't as amused when he insults him a lot on his Julliard past. Nevertheless, once Kyle starts playing he is extremely good and Ephram is intrigued.

Andy is harassing Ephram for being in community college and Kyle is in the room. Amy bonds with a cool teacher at Colorado A&M. She goes to a meeting about a search for the new Provost with a few other women invited by her cool new teacher.

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.