After Lucas and Keith learn that Dan had a heart attack and is still in the hospital, they decide it is best for them to return to Tree Hill. When Deb learns about Haley and Nathan's marriage, she grows hostile. Meanwhile, angry that Lucas left Tree Hill without saying goodbye, Peyton and Brooke try to mend their friendship.
With the assistance of Peyton and Brooke, Lucas throws Nathan and Haley a wedding reception. Although Haley's parents support the marriage, Deb has a difficult time accepting it. Meanwhile, Dan's recent heart attack causes him to try and mend his relationships with Deb and Lucas.
Although Nathan and Haley are already married, Tim insists on throwing Nathan a post-wedding bachelor party, while Brooke throws Haley a bachelorette party. Meanwhile, Lucas tries to decide whether he should visit Dan in the hospital. Karen decides to go back to school. Nathan gets a job working for Keith at Dan's dealership.
Brooke's new neighbor quickly makes his presence felt among the Tree Hill gang and even comes to Brooke's rescue when she is caught shoplifting. Nathan and Haley have their first post-wedding argument when he buys her a gift rather than a much-needed car. Lucas' attempt to help Dan with rehab ends in disaster when Dan reverts to his old ways. Peyton tries to organize an all-ages club and is tempted to try cocaine to seal the deal.
Felix organizes a "dare night" to test the limits of his new classmates. While out playing the game, Lucas meets a mysterious new girl, Anna, and the two of them seem to hit it off. Peyton tearfully confesses to the church that she recently tried cocaine and Keith is caught off guard when a beautiful woman comes to the shop and begins flirting with him. Meanwhile, Karen goes on a date with Andy, her younger professor.
After Dare Night resulted in new arrangements, a midnight meteor shower finds Lucas sharing a romantic night with Anna. Andy surprises Karen with a dinner and Keith cooks for Jules on their first date. Brooke finds herself forming a mutually beneficial relationship with Felix, and Peyton sets out to find an opening act for her club.
The opening of Karen's club "Tric" brings together the people of Tree Hill. Lucas and Felix come to blows over Anna. After Chris quits his gig the night of the club opening, Haley must face her fear of performing to save the night for Peyton. Although Mouth tends to Brooke while she is drunk, Felix sneaks in and attempts to take the credit. Keith and Jules realize their relationship has reached a new level, while Dan deliberately tells Karen that Deb slept with Keith.
The girls of Tree Hill have a slumber party, at which time secrets are revealed and bonds are made. Meanwhile, Nathan and Lucas road trip to Charlotte for a basketball game, and unknowingly to Lucas, they embark upon free HCM tests, a genetic heart condition that Dan maintains. Karen and Andy have a row.
Lucas takes Anna to the formal night but by the end of the night ends up with Brooke. After spending time with Chris, Haley arrives late to the formal which angers Nathan. Meanwhile, Peyton struggles with pressure to do drugs.
Nathan is concerned about Lucas' health, so he tells Karen that Lucas didn't take the heart test. Dan offers Keith to continue working at the dealership-as vice president. At school, Peyton must confront the rumors going around that she is a lesbian. This affects her friendship with Anna. As for Nathan and Haley, they begin to grow apart...
Haley is surprised when her older sister Taylor comes to town, but not as shocked as Nathan, who recognizes Taylor from a past tryst. Brooke and Felix decide to become boyfriend and girlfriend. Jake makes a special visit to Peyton. Anna tells a secret to Lucas.
Nathan comes clean with Haley about his past relationship with Taylor, although Haley continues to email Chris without telling Nathan and Taylor finds out. Lucas and Karen remain at odds over his refusal to take the HCM test. Keith proposes to Jules. Meanwhile, Brooke fights for better working conditions at her new job. Lucas decides to take the HCM test.
When Michelle Branch & Jessica Harp from the band "The Wreckers" perform at TRIC, Haley realizes her passion is to pursue her music career. Meanwhile, Lucas decides to move in with Dan, straining his relationships with both Karen and Nathan. Brooke runs for student council president, but quickly realizes she is taking on more than she bargained for. Peyton and Jake's friendship grows stronger. Brooke finds out that Mouth broke her car window. Lucas gets his HCM results and aren't what they turn out to be.
As his marriage with Haley continues to go wrong, Nathan goes into a emotional crisis and becomes the "bad" Nathan of the past. Karen continues to struggle and try to figure out what would cause Lucas to move in with Dan. Peyton and Jake's relationship gets greater.
When Tree Hill High does a time capsule project, the gang confesses their most intimate secrets to an anonymous video camera. Nathan's anger over Haley's absence continues to grow, landing both Lucas and Nathan in jail. Peyton and Jake's feelings for each other heat up, while Felix throws Brooke a party to celebrate her new gig as student body president. Meanwhile, when brought to court, Lucas opts to live with Dan and Deb rather than Karen.
Keith and Jules' wedding day, and the event has turned the town upside down. Brooke asks Lucas to take her to the wedding as his date, Nathan makes an important decision involving his marriage to Haley, and Jake and Peyton take a big step in their relationship. Meanwhile, Karen and Andy discover Jules' secret relationship with Dan.
Keith gets violent with Dan after learning that Dan paid Jules to fall in love with Keith. Anna turns Felix in to the school authorities after learning that he was the one who vandalized Peyton's locker. Lucas and Brooke discuss Brooke's possible move. Meanwhile, Nathan chances Haley in the hope of bringing her home. Brooke decides to move in with Karen.
On his way home from seeing Haley, Nathan stops to visit Taylor hoping for some fun and maybe more. Meanwhile, Anna gets a surprise visit from her ex-girlfriend and is inspired to tell her parents about her sexuality. Also, Lucas works with Andy to bring Dan down, Karen puts her foot down with Brooke. Peyton and Jake continue to hide baby Jenny from Nicki.
Nathan's Uncle Cooper comes into town to take Nathan and Lucas on a racing trip. On the track, Nathan and Lucas are challenged to a race by the beautiful Daytona and her smart aleck brother Jarret, but things go horribly wrong when Nathan loses control of his car and crashes into a wall. Meanwhile, Deb's addiction to pain pills intensifies and Dan exposes Andy's relationship with Karen to his class.
Lying in a coma after his race car accident, Nathan dreams of what life would have been like if Dan had stayed with Karen and Lucas instead of marrying Deb. In this imaginary world, Lucas would have had the wealth and stature and Nathan would have been the one growing up on the wrong side of the tracks. After waking up, Nathan phones Haley and tells her he doesn't want her to come home.
Nathan is released from the hospital and returns home to a pile of unpaid bills and an eviction notice. Lucas, Peyton and Brooke throw a fundraiser Tric to raise money, but Dan is the one that comes to Nathan's rescue. However, his gift comes with strings - he wants Nathan to ask Haley for an annulment.
Things heat up between Lucas and Brooke after they head to New York for an overnight stay with Haley. Nathan and Deb conspire to desert Dan for good, leading to an explosive conclusion when he discovers their plan. Peyton is elated by getting Jimmy Eat World to perform at TRIC in time for Jake's release from jail. Meanwhile, Andy invites Karen to spend the summer in New Zealand.
