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.

At her father's suggestion, a heartbroken Amy is determined to make the most of her senior year in the wake of Ephram returning from New York and telling her that piano has to be his number one priority. Andy contemplates telling Ephram about Madison's (Sarah Lancaster, who does not appear in the episode) pregnancy. Meanwhile, Rose naively agrees to help Bright find his true calling after she discovers that he hasn't enrolled for college classes and is in fact leading a life of total leisure.
Also, Dr. Jake Hartman (Scott Wolf) creates a marketing blitz for his new practice that threatens to push Dr. Abbott over the edge. Lastly, Nina takes in her friends' teenage daughter, Hannah (Sarah Drew, "Radio"), and asks Ephram to take her under his wing.

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.

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.

Andy worries that Ephram is beginning to question himself and his chances of getting into Julliard after he applies to a college in Colorado as a back-up plan. Similarly, Harold has concerns of his own when Amy informs him that she's not applying to the school they always dreamed of her attending, Princeton, because it would take her too far away from Ephram. Meanwhile, Andy jumps head first into helping Amanda (guest-star Anne Heche) and her disabled husband (guest-star Jason Beghe) with a new therapy involving music, but it may be too much and too fast for Amanda; and Edna and Irv's marriage hits a rough patch after Irv loses his job and they contemplate their future together.

When Jake surreptitiously informs Andy that Ephram came to him for a STD test, Andy and Harold decide the best plan of action is to convince Ephram and Amy to hold off on sex. Of course, when Ephram realizes it's no coincidence that he and Amy both had a heart-to-heart with their fathers on the same day and informs her of his suspicions, Amy feels betrayed that Ephram didn't tell her about the test beforehand.
In another part of town, Nina finally decides it's time to tell Andy how she feels about him and asks him out to dinner, and Bright invites a lovestruck Hannah to go with him to a movie, but the night takes a turn for the worst when Hannah misinterprets his interest.

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.

Amy and Ephram plan a romantic night together at the Abbott cabin in order to take their relationship to the next step. When they arrive at the cabin, and after their parents worrying about how they'll handle having sex, Ephram and Amy worry that their relationship won't be able to handle the next step. Back in Everwood, Andy and Amanda chaperone Delia and Charlie on a date, but the evening takes a bad turn when Andy assumes he's on a date with Amanda; and Nina gets help from Jake after Sam is hurt ice skating and her feelings towards him begin to change.

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.

After Amanda decides to send her husband to a treatment facility, Andy collapses in front of Harold due to all the added stress of the guilt he's been feeling. Meanwhile, Amy continues to shut out Ephram for lying to her about Madison; and Edna makes Irv a writing room, but her seemingly kind gesture causes a fight between the two.

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.

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.

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.

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.

Feeling conflicted over the recent turn of events and not willing to jeopardize Ephram's Julliard audition, an angst-filled Amy tells Ephram that he should take Andy to New York instead of her. In New York, Andy struggles with memories of his former life and the desire to tell Ephram the truth about Madison. Fate plays a hand when Ephram runs into Madison in Manhattan and they make plans to see each other, causing Andy to take matters into his own hands. The episode was partially filmed in New York City.

On the morning of his Julliard audition in New York, Ephram makes plans to meet up with Madison (guest star Sarah Lancaster) for coffee where he finds out that she was pregnant with his child. This devastating revelation causes Ephram to make decisions that will alter the course of his life. Amy tries to figure out what this will do to her and Emphram's relationship. Meanwhile, Dr. Abbott counsels a man (guest star Chris Penn) whose son may die as a result of a hunting accident.

After returning from New York feeling lost and confused and needing Amy for support, Ephram considers his options in the wake of Madison's (Sarah Lancaster, who does not appear in this episode) life-altering revelation. Ephram tries to find the baby by going to Child Services Office, but finds out that Madison signed the adoption papers with "father unknown" and terminating the parent-child relationship with "Unknown Birth Father" leaving Ephram completely crushed.
Amy tries to get Ephram another audition at Julliard after he missed his first appointment due to the emergency with Madison and the baby, but it doesn't go well. Meanwhile, a tired Andy is a little stunned upon learning the extent of Nina's feelings for Jake and with a little encouragement from her friend Bright, Hannah decides to go on a date with a smitten Topher (guest-star Lukas Behnken).

Jake's visiting accountant brother Brian (guest-star Tom Parker) from LA says he sees no future for Jake and Nina, prompting Jake to seek advice from Andy. Also, accepted at Princeton, Amy assumes that her father secretly sent in her application. Lastly, health issues create tension between Rose and Harold, but the tension turns to fear when Harold finds out that Rose has a 3-centimeter long tumor.

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 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.

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.