After spending the summer in Tree Hill with Peyton, Lucas eagerly awaits Brooke's and his mother's return to Tree Hill. Flashbacks reveal Peyton looking for the truth when a mysterious woman arrives at her home claiming to be her mother as well as Nathan revealing to Haley that he's going to High Flyers for the summer. Meanwhile, after the Scott Motors fire, Dan begins his quest to find out who attempted to burn him alive.

As summer draws to a close, Brooke organizes an End of Summer Beach Party but few people are in the partying mood. Nathan returns from his summer away at High Flyers, but is hesistant to let Haley back into his life. Meanwhile, Brooke agrees to date Lucas, but only in a non-exclusive manner; Peyton begins to come to terms after the truth behind her birth mother are exposed; and Dan has a revelation about what happened the night of the fire.

On the first day of their senior year, Nathan and Haley have trouble adjusting as separated spouses. Nathan tries to avoid Haley at school and Haley is forced to deal with classmates teasing her about her tour. Meanwhile, Brooke continues to solely date Lucas non-exclusively, rules which Lucas has a hard time dealing with, and Lucas uncovers a shocking secret about Peyton's birth mother. Elsewhere, Dan confronts who he thinks set the dealership fire only to learn who saved his life.

TRIC throws Tree Hill a masquerade ball and Lucas and Haley see it as a perfect time for Lucas to convince Brooke to date him exclusively and for Haley to win back Nathan. As Fall Out Boy performs, both Haley and Lucas struggle make their plans work and Peyton continues to deal with the new mother in her life. Meanwhile, Dan decides to run for Mayor and agrees to give Deb a divorce as long as she stays his wife through the campaign. However, Dan soon learns that Deb might be more of an opponent than an asset during the campaign.

Basketball season arrives in Tree Hill and the season officially begins with a bang at Midnight Madness. There, Nathan and Lucas clash over Haley and Brooke clashes with Rachel, the new girl who has her eye on Lucas. Meanwhile, Dan's unopposed bid for mayor takes a turn when an unlikely opponent steps forward at Midnight Madness.

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 makes with Ellie. Karen and Deb take their campaigning to new heights.

As the town and the team prepare for the Ravens' first game of the season, Lucas worries that his heart isn't ready for the game especially after finding Brooke in bed with Chris Keller. With Lucas' game lagging, Nathan blames the team's difficulties on the court on him. Meanwhile, Peyton and Haley are able to put their differences aside to help Brooke; and as the mayoral campaign heats up, Dan's campaign turns negative.

On election day, Lucas reveals to the person that set the dealership fire that he knows who tried to kill Dan. Brooke, Peyton and Haley find themselves behind bars and have to call Lucas to bail them out. Meanwhile, Chris Keller convinces Nathan to go with him to a high-stakes poker game where Chris and Nathan are able to come face to face to talk about their differences.

Though Brooke and Lucas have gotten back together, Lucas and Peyton take a road trip together in order for Peyton to find Ellie. There, Lucas reconnects with a friend from his past while Peyton attempts to reconnect with Ellie through music. Back in Tree Hill, Mouth, Brooke, and Haley successfully launch the Clothes Over Bros website, but Brooke is thrown into a panic when the demand for the clothes is far over her supply. Meanwhile, Deb reveals to Nathan that she was the one who tried to kill Dan.

The Ravens lose their second game of the season and Whitey is forced to use tough love to get his team to work together. Peyton and Ellie work together for their benefit album and are able to recruit rock band Nada Surf to be featured on it. Meanwhile, Brooke plans a romantic night for Lucas to thank him for submitting her sketches to the Rogue Vogue fashion competition, but their plans are interrupted when Haley and Nathan get into a fight over birth control.

The Tree Hill High guidance counselor forces the students to think about their futures. Nathan and Lucas both have the opportunity to impress a big-name basketball scout and Nathan is crushed when he has to sit the game out. Meanwhile, Mouth is caught in between Brooke and Rachel; Peyton and Ellie put the finishing touches on their benefit album; and Dan reveals to Haley that Nathan paid Chris Keller to work with her.

When a violent rainstorm causes a blackout in Tree Hill, Haley and Nathan are able to work through their problems and start rebuilding their relationship. In the middle of the rain, Brooke and Lucas resolve their latest problem and finally have a romantic night together. Meanwhile, Mouth spends the blackout with Rachel where he begins to learn more about who Rachel is on the inside; Peyton asks Ellie to tell her the truth about her cancer; and Keith and Karen are able to spend some time alone together.

Brooke heads to New York for the Rogue Vogue fashion show where she encounters a life very different from her own -- a whirlwind life of non-stop partying, drinking and drugs that makes her think about what she really wants the most. At the annual Secret competition, Nathan and Lucas reevaluate their own lives after spending the night with the family of an old friend. With Brooke in New York, Rachel takes over as head of the squad and Peyton joins her for a night of drinking to get over Ellie's death. Meanwhile, much to Rachel's dismay, Brooke decides to leave New York to be with her friends at the competition, which the squad ends in style, and Haley and Nathan use their hotel room as the honeymoon suite they never had.

When last year's time capsule is released, everyone's secrets are revealed, forcing Lucas and Mouth to confront the anger of a person from their pasts. Brooke suspects that she knows who released the capsule, but has to deal with what she exposed on the time capsule. Meanwhile, Nathan's entry forces him and Haley to talk about the person Nathan became when she left; and TRIC hosts the breast cancer benefit concert where Haley performs for the first time since she came back to Tree Hill alongside Fall Out Boy and Jack's Mannequin.

Lives hang in the balance when a student brings a gun to school. In the mayhem resulting from the first shot fired, Brooke is able to get out of the school, but leaves Peyton behind. Nathan and Lucas run back into the line of fire to protect Haley and Peyton. There, Peyton reveals her true feelings for Lucas; and Nathan and Haley become trapped with other students and the gunman in the tutor center. When the situation is over, two lie dead and the lives affected will never be the same.

Tree Hill comes together to cope with the school shooting tragedy that resulted in two deaths. Dan grapples with the guilt of murdering Keith after Keith's funeral. With this guilt, Dan attempts to make up time with Lucas and Karen, but Karen's anger towards him only adds to the guilt. Meanwhile, Nathan and Haley see that life is too short to be apart and decide to live together again. Elsewhere, at a party thrown at the school to help ease the pain of the shooting, Mouth learns who really released the time capsule; Brooke is hurt when Lucas isn't able to talk to her about Keith's death; and Lucas disobeys Karen and attends Jimmy's funeral.

The kids load up and head out to Rachel's cabin for a weekend to kick back and heal after the tragedy that rocked Tree Hill. There, Nathan decides to propose to Haley, but has trouble getting her wedding ring away from her to do so. Fall Out Boy's Pete Wentz shows up in order to spend more time with Peyton, much to the shock of the others, and Mouth and Rachel are able to talk about the release of the time capsule. Meanwhile, Skills and Bevin get lost in the woods; Karen lets her anger out on Dan; and Nathan is finally able to have the perfect moment he planned with Haley.

Lucas takes the court for the first time since Keith's death, but finds it impossible to play. Brooke uses materials she stumbled on at the cabin to seek revenge on Rachel, but ends up angering Mouth and pushing Mouth and Rachel closer together. Meanwhile, Nathan and Haley begin to plan their recommitment ceremony but are stunned when they fail a compatibility test. Peyton debates whether or not to head to Chicago to spend the weekend with Pete Wentz and ends up running into a person from her past at the airport.

At the league tournament, Nathan and the team have to find a way to win with Lucas no longer on the team. At the tournament, Nathan has to deal with an old rival both on and off of the court. Brooke and Mouth stumble across a plan to get back at Rachel. Meanwhile, Deb and Nathan get a restraining order against Dan; and Peyton, in Savannah with Jake, is left with a decision that could change the course of her life.

With the re-commitment ceremony rapidly approaching, Brooke agrees to make Haley's dress, but the final product is less than flattering. Brooke takes charge of the rehearsal dinner and puts her own unique spin on the event. Meanwhile, Peyton has to confront her feelings for Lucas; and Brooke comes up with a special way to fix Haley's wedding dress.

On the day of their re-commitment ceremony, Nathan can't shake the feeling that something horrible is about to happen to Haley. The ceremony goes as planned until Rachel gives a drunken speech about Cooper and a series of events leads to a possibly tragic event. Elsewhere, Lucas stumbles upon two pregnancy tests, one of which he learns is his mother's; and Peyton and Brooke's relationship falls apart when Brooke learns about Peyton and Lucas' kiss during the shooting.