After spending the summer out of town, Brooke returns to Tree Hill. Lucas welcomes his mother at the airport. Peyton investigates a mysterious woman who claims to be her mother. Meanwhile, Nathan must deal with Haley's reappearance and the aftermath of the fire at Scott Motors. Dan's fate after the fire is revealed.
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Brooke organizes a beach party to celebrate the end of summer but soon finds she's the only one in a party mood. Nathan comes home to reconnect with Haley, but now he and Lucas aren't getting along. Meanwhile, Lucas struggles with Brooke's new rules for dating, and Peyton tries to come to terms with the newly discovered secrets about her family. Finally, Dan remembers what happened the night of the fire at his dealership.
On the first day of senior year, estranged spouses Nathan and Haley have trouble adjusting as classmates. While Brooke continues to play hard-to-get, Lucas learns a troubling secret about Peyton's mom. Meanwhile, Dan starts to uncover the truth about the dealership fire.
It's party time in Tree Hill. A masquerade ball at the club Tric provides the perfect opportunity for Haley to win back Nathan's heart and for Brooke to seduce Lucas. Members of the punk-pop sensation Fall Out Boy perform amidst the costumed madness, while Peyton tries to accept her recently revealed birth mother. Meanwhile, Dan gives Deb an ultimatum, but he soon discovers she's a much more worthy opponent than he thought.
The Ravens officially begin basketball practice - with explosive results. Nathan, the new team captain, clashes with Lucas over Haley. Brooke selects Rachel to fill a vacancy on the cheerleading squad but regrets her choice when the new girl is noticeably interested in Lucas. Meanwhile, Dan's bid for mayor takes a surprising turn when an unlikely opponent steps forward.
In an effort to keep her cheerleaders from fighting over the same guys, Brooke devises a "Fantasy Boy Draft." Haley and Peyton butt heads over Nathan, while Lucas has trouble keeping up with the brutal pace of basketball practice. Meanwhile, as the election nears, mayoral candidate Dan clashes with his new opponent.
As the fantasy draft dates begin, Brooke finds herself on an unusual double date, while Lucas gets closer to Rachel. Mouth spends time with an old friend, and Peyton regrets choices she has made. Karen and Deb take their campaigning to new heights.
As the town readies for the Ravens' first basketball game, Lucas worries about his lack of commitment to basketball. Nathan accuses Lucas of being the team's weakest link. Peyton and Haley ignore past differences to support Brooke in a time of need. When the mayoral race tightens, Dan resorts to a smear campaign.
Lucas reveals that he knows who tried to kill Dan. Brooke, Peyton and Haley find themselves behind bars. Chris Keller convinces Nathan to help him at a high-stakes poker game. And 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 web site, only to find that demand far exceeds supply. Deb reveals to Nathan that she tried to kill Dan.
After losing their second game of the season, the Ravens receive tough love from Whitey. Peyton and Ellie try to recruit rock band Nada Surf for their benefit album. Haley reveals a disturbing fact to Nathan, and Brooke plans a romantic night for Lucas after learning that he submitted her fashion designs to a prestigious competition in New York.
When a guidance counselor challenges the students of Tree Hill to consider their futures, Nathan and Lucas feel pressured to impress an important basketball scout. Mouth gets caught between Brooke and Rachel. Peyton and Ellie grow closer while finalizing their CD. And Dan tells Haley that Nathan paid Chris Keller to come back into her life.
A violent rainstorm knocks out the power in Tree Hill, leading Haley to Nathan's doorstep and Brooke into the downpour for a dramatic confrontation with Lucas. Peyton finally confronts the truth about Ellie's 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 must 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 reveals the contents of the students' time capsule, 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. And Haley is forced to reconcile the man Nathan used to be with the man he has become.
A normal day becomes deadly when a despondent student brings a gun to Tree Hill High. While lives hang in the balance, Nathan and Lucas put themselves at risk to protect their friends and loved ones.
The aftermath of the school shooting forces the residents of 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. And Lucas and Peyton consider the implications of their kiss in the library.
Rachel invites the gang to her family's cabin for a weekend getaway. Lucas, Brooke and Nathan conspire to surprise Haley, while Peyton receives an unexpected visitor at the cabin. Mouth harbours resentment towards Rachel, and a game of "I Never" reveals a secret.
Lucas struggles with whether or not he should play basketball now that Keith is dead. Brooke forces Rachel to deal with a dark secret. Nathan and Haley's reprise wedding plans are put to the test. And Peyton decides to go to Chicago and visit Pete Wentz of the band Fall Out Boy.
It's the weekend of the Coastal Classic basketball game, and with Lucas sidelined, Nathan has to step up on the court against an old rival who shows an interest in Haley. Brooke and Mouth plot revenge against Rachel while Dan goes head to head with Nathan's uncle.
On the night before Nathan and Haley's wedding, Brooke argues with Haley over the wedding dress. Meanwhile, Lucas and Karen return to Tree Hill, and Peyton makes a startling discovery.
In the season finale, Nathan worries for Haley's safety, and Peyton and Brooke's friendship is tested prior to the wedding. Meanwhile, Deb tells Dan the truth about the dealership fire. And Karen finds herself needing Keith more than ever.