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.

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.

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.

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.

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.

Andy's father, whom the Brown's haven't seen in 15 years, pays a visit to Everwood surprising Andy, Ephram and Delia. Ephram and Amy try to cheer Bright up and take him out to celebrate his 21st birthday. This ends badly when a drunk Bright falls through a window and ends up in hospital. Hannah rushes to Bright's side, leaving Nick behind on their date. Jake's big question last week, gets an answer from Nina as she has decided to move to LA. Andy is not happy about this. Edna and Irv decide to drive all over the country for their retirement.

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.

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 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.

A heartbroken Ephram finds himself the odd man out as Amy prepares for Colin's homecoming. Meanwhile, Andy and Dr. Abbott join the town in a debate over the use of medicinal marijuana after a large quantity is discovered in a deceased woman's greenhouse; and Andy provides medical guidance to Nina after her son's teacher suggests she put him on Ritalin.

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.

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.

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.

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.

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

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

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.

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 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.