In the second season premiere, Lucas and Keith learn that Dan suffered a heart attack and decide it is best for them to return to Tree Hill. Peyton and Brooke continue to mend their broken friendship as they both cope with the loss of Lucas. Meanwhile, when Deb discovers that Nathan and Haley have married, she is less than thrilled for the happy couple.
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 bash, while Brooke gives Haley a bachelorette party. Meanwhile, Lucas debates whether to visit Dan in the hospital, Karen decides to go back to school, and 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 an expensive gift rather than a much-needed car. Lucas' attempt to help Dan with rehab ends in disaster when Dan reverts to his old persona. Meanwhile, Peyton tries to organize an all-ages club and is tempted to try cocaine to seal the deal.
Felix puts together a "dare night" that tests the limits of his new classmates. During the game, Lucas meets a mysterious new girl, Anna, who is connected to the gang in a way they don't yet know while Peyton confesses to the church that she recently did cocaine. Meanwhile, Keith is caught of guard when a beautiful woman comes to the dealership to buy a car and the two end up hitting it off and Karen goes on a date with her professor, Andy.
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 all-ages club "Tric" brings drama and discord to the Tree Hill crowd. After Chris quits his gig on the night of the club's opening, Haley must face her fear of performing to save the night for Peyton. Mouth tends to a drunken Brooke, but Felix steals the credit and feelings begin to develop between the former friends-with-benefits couple. Meanwhile, Felix and Lucas come to blows over Anna; Keith and Jules reach a new level in their relationship; and Dan deliberately tells Karen about the night Deb and Keith spent together.
The girls of Tree Hill have a slumber party, at which time secrets are revealed and bonds are made. Meanwhile, Nathan and Lucas embark on a road trip to Charlotte for a basketball game, and unknowingly to Lucas, are scheduled to be tested for HCM, a genetic heart condition that Dan carries. Meanwhile, Karen and Andy have their first fight.
Lucas takes Anna to the formal night but at the end of the night, someone else is in his arms. And when Brooke finally learns the truth about who took care of her the night she got drunk, her relationship with Felix comes to an immediate end. Haley arrives late to the formal which angers Nathan, especially when he discovers that she's been spending time with Chris. 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 the chance to continue working at the dealership - as vice president. Meanwhile, Peyton must confront the circulating rumors that she is a lesbian, and Nathan and Haley's relationship continues to deteriorate.
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 an official couple. Jake makes a special visit to Peyton. Anna tells Lucas a shocking secret.
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 "The Wreckers" perform at TRIC, Haley realizes her passion is to pursue her music career. 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. Meanwhile, Brooke finds out who really broke her car window and Lucas gets the results of his heart test.
As his marriage continues to crumble, Nathan goes into a emotional crisis and reverts to his past bad behavior. Karen continues to struggle with Lucas' decision to move in with Dan and wonders what hold Dan has over their son. Meanwhile, Peyton and Jake's relationship grows deeper.
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.
It's 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 about his marriage, and Jake and Peyton take a big step in their relationship. Meanwhile, Karen and Andy discover Jules' secret relationship with Dan.
Keith gets unhappy 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.
In the first part of the two hour second season finale, things heat up between Lucas and Brooke after they head to New York for an overnight stay with Haley. Peyton is elated when she gets the band 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.
In the second part of the this seamless 2-hour Season Finale of "One Tree Hill," things heat up between Lucas and Brooke since he finally tells her what he feels about her. Nathan and Deb conspire to desert Dan for good, leading to an explosive conclusion when he discovers their plan. Peyton has a shock. Meanwhile, Karen decides to spend the summer holiday in New Zealand. And at the climax of Dan's numerous deceptions someone sets the dealership on fire with him in it.