In the third season premiere, we finally discover Dan's fate after the fire. Besides the situation with his father, Nathan also has to deal with Haley's reappearance in Tree Hill and the future of their relationship. Meanwhile, Peyton tries to find the truth about the mysterious woman who pretends to be her mother. Also, Lucas looks forward to Brooke's return after a summer apart.
Brooke has a end of the summer party on the beach; Nathan is home from basketball camp; Lucas deals with Brooke's rules for dating; Peyton deals with family issues; Haley tries to tell Nathan how she feels.
Nathan asks Haley for a possible divorce. Lucas tells Dan that he saved his life. Peyton finds out something deep about Ellie. Dan tries to drop accusations at several people about the fire. He also tries to get Whitey replaced as Ravens coach.
It's Halloween in Tree Hill and everybody is celebrating at Tric, with special guest band Fall Out Boy. The masquerade ball gives the opportunity to Haley to win back Nathan while Brooke is trying to seduce Lucas. Also, Peyton decides to face her new mother and get to know her; Dan uses blackmail to become mayor but things don't turn out as easy as he thought they would when Deb gets in his way.
The Ravens begin basketball practice. New team captain Nathan clashes with Lucas over Haley, and a new cheerleader sets her sights on Lucas. Elsewhere, Dan's mayoral bid takes a surprising turn when an unlikely opponent emerges, Karen.
Brooke makes a "Fantasy Boy Draft," after all of the cheerleaders are fighting over the same guys. Haley and Peyton continue to argue over Nathan. Dan butts heads with Karen because the election is drawing nearer. Lucas is trying to keep up with the fast pace of basketball.
The fantasy draft dates begin, Lucas finds himself with Rachel and a very familiar setting. Brooke is on a double date with an unusual couple. Mouth and Peyton hang out again. And Peyton regrets the things she says to Ellie. Karen and Deb take the campaigning for mayor, to a new level, to bring down Dan. Nathan gets mad when Chris gets close to Haley.
As the town readies for the Ravens first basketball game, Lucas worries that his head and heart aren't in it. Nathan accuses Lucas of being the Ravens' weak link. Peyton and Haley mend fences to support Brooke in a time of need. When the mayoral race tightens, Dan resorts to a smear campaign.
It is revealed that Lucas knows who tried to hug Dan and he confronts the guilty party. Brooke, Peyton and Haley find themselves behind bars. Peyton finds her guilty conscience on the surface. Chris Keller convinces Nathan to be his wingman at a high-stakes poker game. The residents of Tree Hill finally choose a mayor.
Lucas and Peyton take a road trip together to find Ellie. While out of town, Lucas reconnects with a friend from his past. Brooke, Haley and Mouth successfully launch the Clothes Over Bro's website, only to find that demand far exceeds supply. Deb reveals to Nathan that she tried to hug Dan.
The Ravens lose their second game in a row, so Whitey teaches them a tough lesson. Peyton and Ellie look for support for their album and hope to attract Nada Surf to the project. Meanwhile, both Dan and Haley upset Nathan, while Brooke plans a romantic thank-you for Lucas.
As the students meet with the school counselor to plan for the future, Nathan and Haley realize they want to attend different colleges across the country from one another and Brooke discovers Rachel's reasons for submitting her designs to Rogue Vogue. Meanwhile, Ellie and Peyton bond as they finish the benefit album.
A unhappy rainstorm knocks out the power in Tree Hill, leading Haley to Nathans doorstep and Brooke out into the downpour for a dramatic confrontation with Lucas. Peyton finally confronts the truth about Ellies illness, while Mouth is tempted by his new friend, Rachel. Before morning, secrets are revealed, relationships are tested, and new love gets hotter than ever.
Brooke is forced to grow up in a hurry when her trip to a New York City fashion show prevents her from attending an annual cheerleading tournament. Nathan and Lucas are influenced by the father of an old friend. Struggling with her mother's cancer, Peyton joins Rachel for a night of blowing off steam, and Haley and Nathan use their hotel room as the honeymoon suite they never had.
When someone unleashes the students' time capsule upon Tree Hill High, Lucas and Mouth must confront a person from their past. Brooke has to deal with the revelation that secrets aren't the only things she exposed in the time capsule. Dan learns to forgive Keith. Haley is forced to reconcile the man Nathan was before with the man he has become, and Peyton's Breast Cancer Benefit Concert at Tric features performances by Haley, Jack's Mannequin and the return of Fall Out Boy.
Due to the aftermath of the release of the time capsule, chaos breaks out. Someone is holding students of Tree Hill hostage with a gun, shooting. While lives hang in the balance, Nathan and Lucas put themselves at risk to protect their friends and loved ones. Young lives are shattered and two lives will end.
The aftermath of the school shooting and the death of Jimmy Edwards forces everyone in Tree Hill to examine their lives. Nathan reassesses his relationship with Haley, while Brooke and Rachel join forces to heal the student body. Dan must deal with the ramifications of shooting Keith, while Lucas and Peyton consider the implications of their kiss in the library.
Rachel invites the gang for a weekend getaway at her family's cabin. Craziness will ensue, including a game of "I Never" which will cause characters to do things they normally wouldn't, and a nasty little issue Mouth has been harboring toward Rachel will surface. Meanwhile, Karen will confront Dan about Keith's death. Could she suspect the truth?
Lucas attempts to play in the first game after Keith's death, but cannot bring himself to do it; Nathan and Haley prepare to renew their vows, while Mouth tries to get closer to Rachel; Peyton receives a surprising offer; and Brooke finds a way to get revenge on Rachel.
Nathan deals with a player who is a rival both on and off the court; Brooke and Mouth look to get even with Rachel; Dan has a run-in with Cooper; and Peyton comes to a major decision.
Haley argues about her wedding dress with Brooke during the rehearsal dinner; Karen and Lucas arrive back in town; and Peyton is surprised by what she finds.
Nathan worries about Haley as they prepare to renew their vows; Deb confesses to Dan about the fire; and Peyton and Brooke's friendship becomes strained.