Lucas waits for Brooke to return to Tree Hill from her summer with Peyton. Peyton tries to find out more about the woman who says she is her mother, while Haley’s own return has Nathan thinking about their future together. Meanwhile, the fire at Scott Motors, which Dan survives with only minor injuries, has its aftermath.
Brooke’s party to say goodbye to summer lands with a thud when she finds that none of her guests are in the most festive of spirits. Lucas is frustrated, himself, when Brooke sets guidelines for him with regards to having a relationship with her.
Senior year begins, but Nathan and Haley find it awkward settling in as classmates again. Lucas learns some upsetting news about Peyton's mother, while continuing to pursue Brooke, who is playing it cool. Dan, meanwhile, continues to piece together the events of the blaze that consumed the dealership.
Haley uses a masquerade party at Tric to try and get back in Nathan’s good graces, while Brooke takes the opportunity to try and make a play for Lucas. Meanwhile, Peyton tries to get adjusted to the presence of a mother again and Dan is taken aback when Deb starts giving the hardball tactics as much as she gets them.
As the Ravens' basketball season begins, new captain Nathan and Lucas have words about Haley, which turns into a fist fight that spills out onto the court. Brooke wishes she hadn't decided to accept a slot on the cheerleading squad when she is forced to watch a new girl, Rachel, vie for a slot in Lucas' heart. Meanwhile, Dan's plan to run for mayor is thrown for a loop when a surprising candidate jumps into the race.
Brooke designs a mock draft based on the basketball team players' attractiveness for the cheerleaders in the hope that they won't squabble over which ones to date. Lucas finds it increasingly difficult to maintain his stamina during the harsh practice regimen. Meanwhile, Haley and Peyton have some differing thoughts about Nathan which result in an argument, and Dan's political opponent in the mayoral race shows a tougher side.
Brooke's fantasy draft heats up as she ends up on a date with not one, but two, participants. Lucas and Rachel begin to connect, while Peyton begins to lament her soured relationship with Ellie. Meanwhile, Mouth finds comfort in an old friend, and Deb and Karen begin hitting the campaign trail as the mayoral race progresses.
Lucas begins to think he's just not into playing basketball as the Ravens' season opener comes around, which leads Nathan to come down on him as the team's Achilles' heel. Meanwhile, Brooke finds emotional support from the warring pair, Peyton and Haley, while Dan begins to play dirty to help steer the election his way.
Lucas comes clean about the person he is confident tried to murder Dan. Brooke, Peyton and Haley end up in jail. Meanwhile, Nathan is coaxed by Chris into attending a big money poker game, and Tree Hill wraps up its mayoral election.
Lucas joins Peyton and the two hit the road in search of Ellie, during which time an old friend of Lucas' comes into the picture. Nathan is shocked by Deb's admission of her attempted murder of Dan. Meanwhile, Brooke, Haley and Mouth start up the Clothes Over Bro's clothing website and find themselves besieged by orders.
Whitey comes down on the team after an excruciating Ravens loss. Peyton and Ellie try to get Nada Surf to play on a benefit CD. Meanwhile, Lucas sends Brooke's fashion designs to a competition, prompting her to go all out for a night alone with him, and Nathan is shocked when Haley drops some heavy information on him.
Nathan and Lucas think about making a good impression on a basketball recruiter when a school counselor gets the students to consider their direction in life. Peyton and Ellie complete work on their album. Mouth finds himself in the middle of the drama between Peyton and Rachel. Meanwhile, Dan informs Haley that Chris was enticed to come around again at Nathan's paid request.
The power goes out in Tree Hill during a massive storm, and things get a little stormy on on the personal front as well. Haley finds herself at Nathan's place, and Brooke braves the elements to have some serious words with Lucas. Peyton and Ellie also find themselves together and having a frank discussion about Ellie's condition. Meanwhile, Rachel becomes a tantalizing option for Mouth.
Brooke's trek to New York City forces her to miss a major cheerleading competition. A friend's father causes Nathan and Lucas to reevaluate life. Meanwhile, Haley and Nathan take a belated honeymoon in their hotel room, and Peyton decides to go out for a night on the town with Rachel to ease the pain of losing her mother.
Lucas, Mouth and Brooke are forced to revisit the past when Tree Hill's time capsule is suddenly unearthed. Meanwhile, Haley must come to terms with the changes in Nathan, while Dan tries to get over his grudge with Keith, and Peyton successfully stages her benefit for breast cancer.
A student teetering on the brink of despair comes to school with a gun and begins shooting. Lucas and Nathan go into the building to try to find their friends, stuck somewhere inside. While Lucas finds an injured Peyton in the school library, Nathan, Haley and several others find themselves trapped in a locked down room with the shooter.
In the wake of Jimmy Edwards' and Keith's deaths, Tree Hill feels a jolt and tries to make sense of their own lives. Brooke and Rachel attempt to ease their classmates suffering. Nathan takes another look at his love for Haley, while Lucas and Peyton think about whether or not they should follow up on their kiss together. Meanwhile, Keith begins to feel haunted by his killing of Keith.
Everyone decides to come together for a weekend retreat at Rachel's family cabin. Brooke and Nathan make it a point to surprise Haley there and Peyton is shocked when an unannounced guest turns up, while Mouth stews over a lingering gripe with Rachel. Meanwhile, Dan finds himself interrogated by Karen about Keith's death.
Lucas tries to figure out whether or not to carry on with basketball in the aftermath of Keith's death. Brooke coaxes Rachel into confronting her own darkness. Meanwhile, Nathan and Haley try to make their marriage work, while Peyton takes a trip to see Fall Out Boy’s Pete Wentz in Chicago.
Nathan is called upon to bring his best game to the Coastal Classic as Lucas is forced to sit on the bench. Nathan's opposing team rival is eager to do the same and to woo Haley. Meanwhile, Brooke and Mouth prepare a comeuppance for Rachel, Peyton makes a difficult, but bold decision about her life and Nathan's Uncle Cooper and Dan butt heads.
Brooke and Haley get into a spat over the subject of Haley's wedding dress as the eve of the rehearsal dinner comes around. Meanwhile, Peyton learns some surprising information and Lucas and Karen make their way home to Tree Hill.
Nathan comes to believe that Haley may be in harm’s way on the day of their second wedding. Peyton and Brooke's friendship comes to an end as Brooke's anger at Peyton over Lucas comes to a boiling point. Meanwhile, while Karen finds herself more and more alone without Keith, Dan has a feeling of dread when Deb secretly tells him that she, not Keith, was the one who tried to kill him.