Dr. Andy Brown agrees to operate on Colin once again. But the Risky surgery goes wrong and Colin’s fate is decided. He doesn’t live through the operation. Because of this, the complete town of Everwood shuns the Brown family. Dr. Brown is devastated with guilt of not being able to save Colin. He regrets the promise he gave to Colin to bring him back. Amy confronts Dr. Brown for this.

Ephram has his eye only on one college: Julliard and is completely focused on the auditions. However, Dr. Andy Brown has started to feel that Ephram would need more extracurricular activities to get into the best college. But the Julliard auditions have surprising results. Amy’s mother is concerned when she notices Amy’s lack of interest in preparation for college admissions. Bright’s future is at risk because of his poor grades.

The Abbots are shocked when Dr. Linda Abbot, Harold's sister, returns to town after practicing medicine around the world. In all the excitement, Edna doesn't see that her relationship with Irv is suffering while Harold's excitement is cut short when Linda tells him that she wants to join his practice. Meanwhile, Andy talks to the parents of pre-teens who have been practicing unsafe sex and is shocked by their reaction to the situation; and Bright asks Ephram to look out for Amy.

Andy's plan to ease Ephram's load by hiring a caretaker, Madison Kellner, for Delia backfires when Madison treats Ephram like a child in front of Amy, embarrassing Ephram. Meanwhile, Andy, focused on Colin's father's alcoholism, doesn't realize Nina's need for a friend after her divorce; and Linda and Harold's differences clash at the office.

Dr. Andy Brown invites Linda Abbott over for dinner. The main purpose was to discuss a patient with her. But when Delia witnesses the dinner, she has a completely different perception about it and starts cursing Linda. Ephram talks to Madison and figures out the reason for Delia’s behaviour. Amy becomes more depressed. The therapist suggests medication but Dr. Abbott refuses to write a prescription for his daughter.

Dr. Abbott feels that Linda is attracted to Dr. Brown. So, he plans to match her with a more suitable man Ephrams gathers strength and confesses his feelings to Amy. But he gets confused when he realizes his feeling for Madison as well. Madison helps Ephram to pass his driving test. Reverend Keyes is to be married soon. Dr. Brown tries to help him with his blindness but Reverend would rather leave his fate to God over getting a treatment.

A coal mine collapses near Everwood. Dr. Brown, Dr Abbott, Dr. Linda and Edna rush to the site of accident to provide medical help. One Miner is Ephram’s mentor, Will Cleveland. Another is Abbot’s Next door neighbour and the third miner is Ellie Beels, Andy’s patient wants to conceive a baby. Each of the doctors is using their special skills to save them. But Andy needs to confront his biggest fear to save their life.

After the town mechanic diagnoses a patient of Andy's with meningitis rather than flu, the townspeople begin to think that he has a special gift. Meanwhile, Ephram tells Madison about his feelings for her; Amy goes to Linda for help with her depression; and Edna learns the disturbing truth about why Linda refuses to date Andy.

Dr. Brown starts to pursue Linda even after knowing Edna’s and Harold’s objections. He finds out the reason for their objection when Linda confesses that she has H.I.V.Bright tells Ephram that he can win Madison’s heart if he shows ignorance towards her. But the complete plan fails when she has a break up with her boyfriend. Amy meets Tommy Callahan and soon falls for him because of his understanding of her depression.

Shocked after learning about Ephram and Madison's relationship, Andy debates whether or not to fire Madison, but his mind is made up for him when Madison decides to quit. Her leaving upsets Delia, making for an unhappy holiday season. Meanwhile, Harold is upset when Amy brings Tommy over for Thanksgiving, leading to Amy running away from home.

The promise Andy made to Delia that he would never date Linda Abbott is broken. And a rift is created in his relationship and Delia. He plans to take Delia on a bonding trip to earn her trust again. Andy gets into tough situation when a woman patient approaches him to get pregnant by in-vitro fertilization with his husband’s sperm but he is already dead.

Dr. Andy Brown tries to help a high school wrestling Champion when his bulimic habits put his life in dangerous situation. Bright gets into a fight with Amy’s boyfriend, Tommy Callahan and is suspended from the school for this. Linda worries that because she has HIV, Andy doesn’t want to get intimate relationship with her. And finally, Ephram is convinced that Madison is embarrassed to be seen with him.

Amy relationship with her parents is healing slowing but the situation is worsened when she forgets about Dr. Abbott’s birthday dinner. Ephram writes a love song for Madison and Madison lies to him that she likes it. Ephram wishes to her to show the song to her band. But she refuses and they end up fighting on this. Nina decides and confronts Andy about ignoring her friendship over his relationship with Linda.

Madison tells Ephram that her room mate is going out of town. Ephram gets a wrong idea of her telling him about it. But the confusion leads to a romantic night for the couple. Amy feels tat she is ready to have sex with Tommy and gathering her strength asks dr. Brown to prescribe her birth control pills. Andy makes an important decision to talk to Ephram and Delia about Linda.

On an impulse, Ephram confesses to Madison that he loves her. But he is heartbroken when she doesn’t respond the same. Since Andy needs to go with Ephram and his piano teacher to Boulder for a competition, Linda agrees to take care of Delia for the meanwhile. Amy realizes that she can never trust Tommy again and eventually they have a break up.

Madison is performing with a band in a bar. In order to get Ephram in the bar so that he can watch her performance, he and Bright work on getting Ephram a fake id. After getting the divorce, Nina turns to Andy for emotional support. And seeing their closeness, Linda is getting suspicious. In the mean time, Dr. Harold and Rose schedule to meet Amy’s guidance counselor because of her poor grades.

Amy returns to her home but she finds it very difficult to adjust to her old life again. The situation gets more complicated when Dr. Abbott and Rose find out that Amy is taking birth control pills. Her old friends also are not that glad to welcome her back. Meanwhile, Ephram is worried when he feels that Madison is going to break up with him. Andy testifies on behalf of Nina in her battle to take the sole custody of her son.

Although Andy doesn’t support the idea, but Ephram and Madison determine that it would be better if Madison resumes her job of Delia’s caretaker. Amy is confused to decide that would it be better to go off her anti depressant medication. In Linda’ opinion Amy is ready to stop the medicines. Bright is anxious and waits for the letters of his acceptance to college.

Amy talks to Bright and accepts that she may have feelings for Ephram. Bright suggests her to rather show mercy on Ephram as he is already suffering from his break up with Madison. When Delia confronts Linda about her regular medicines, Linda finally tells her that she is infected with HIV. Delia handles the news better than expected of her. But soon the secret accidentally is revealed to the whole town. Dr. Abbott faces a malpractice suit.

Ephram and Amy go with each other to prom as friends, but Amy has a hard time revealing her true feelings to Ephram. Meanwhile, after the news of her H.I.V. was exposed to the town, Linda decides that it might be time to leave Everwood; and Andy is asked by his mentor to perform a risky surgery on a patient. The only catch is that the patient is the mentor himself.

Amy and Ephram travel to Boulder for Ephram's Julliard audition and during the trip Amy finally tells Ephram about her real feelings for him. Back in Everwood, Andy talks to his mentor about the risk involved with the surgery he wants Andy to perform on him; Harold faces losing his practice when he learns he's not insured against malpractice; and Bright, much to the disappointment of his family, decides not to attend graduation.

Ephram's spirits are high when he learns that he's been accepted into Julliard's summer program. However, Ephram is forced to make a big decision when Amy shares her feelings for him and asks him to stay in Everwood with her. Meanwhile, Harold opens a bagel shop after losing his malpractice lawsuit; and Madison visits Andy with shocking news.