The aftermath of the post-wedding car accident unfolds. Haley is deeply affected by Nathan's attempt to rescue Cooper and Rachel, Brooke confronts Lucas with her true feelings and Peyton makes a startling discovery. Pressured by the fact that someone might know he killed his brother, Dan assaults Deb.
As Nathan, Rachel and Cooper's lives remain precarious following the car accident, Brooke celebrates her 18th birthday but finds it diminished by her struggles with Peyton. Lucas and Karen come to terms with her pregnancy and with the pregnancy of someone close to Lucas, while Deb's past addictions intersect with Haley in an explosive manner.
Lucas and Brooke, now broken up, clash at a post-game party and Haley realizes that Rachel is plotting to seduce Nathan. Meanwhile, Peyton connects with her half-brother, Rachel reveals that she knows who is pregnant and Skills takes the court with the Ravens basketball team.
Peyton introduces hip-hop sensation Lupe Fiasco at Tric, while rumors that Brooke is pregnant run rampant. Still dealing with their car accident, Nathan buys a motorcycle despite Haley's reservations, and Rachel poses for Maxim magazine. Meanwhile, Lucas clashes with Derek, and Deb double-crosses Karen.
Peyton finally realizes that her brother Derek isn't her real brother but in fact the very same person that's been sending her online messages using the alias "watchmewatchyou". When she learns this and starts pushing him away, Derek breaks into her house and tries to hurt her. She is saved in the last minute by her real brother Derek and Lucas. In the end, Derek disappears after surviving a bad fall through Peyton's window.
Nathan and Haley's financial struggles force Nathan to approach Dan for help. In spite of his heart condition, Lucas decides to rejoin the Ravens, teaming him with Skills. Feeling isolated and alone, Peyton finds comfort from an unlikely source, while Brooke begins dating again, but discovers that her new boyfriend is not all that he seems to be. Mouth receives an unexpected proposal, and an old acquaintance of Dan's, Daunte, shows a sudden interest in Nathan.
Brooke has her hands full with her model for the T.A.R.T. fashion show and a new boyfriend. Rachel makes the cover of "Maxim," causing chaos at Tree Hill High. Meanwhile, Lucas learns of Nathan's dealings with Daunte, and ultimately has to choose between Nathan and his love for basketball. Haley takes on a babysitting job only to find herself in over her head and Peyton's half-brother, Derek, forces her to confront her deepest fears.
Derek convinces Peyton to take a chance with Lucas at the same time that Brooke approaches him about getting back together. Daunte's latest demand leads Nathan to seek help from an unlikely source - Dan. When Rachel learns of a failing grade, she turns to Haley for tutoring. Nathan is named MVP of the Ravens at the annual sports banquet.
As Whitey's last game approaches, the residents of Tree Hill feel the pressure of a looming State Championship. Peyton reveals to Lucas that she has feelings for him. Haley learns the sex of her baby. Nathan and Lucas clash over personal and team goals. Karen shows Deb tough love, while Dan tries to strike a bargain with Daunte.
Lucas receives an unlikely visitor -- his supposedly dead Uncle Keith. Haley's life and the life of her unborn child are threatened when she experiences serious complications with her pregnancy and Nathan wrestles with the guilt and consequences of his dealings with Daunte.
Following his heart attack, Lucas returns to school, hoping to rekindle his romance with Peyton. Haley learns that Nathan was responsible for her accident. Brooke and Rachel hatch a plan to steal the next calculus exam, while Dan faces murder charges and Deb breaks out of rehab.
With senior prom only weeks away, Haley's frustration over her injuries increases and Skills and Mouth hatch a plan to help Nathan earn money for the big dance by stripping. Brooke betrays Rachel in order to get closer to a new guy and Peyton and Lucas resolve to be happy. Struggling with her drug addiction, Deb makes a choice that could end her life.
A class assignment reveals the deepest secrets and desires of Lucas and the students at Tree Hill High. Worried about college prospects, Skills turns to Haley, while Nathan wrestles with Deb's suicide attempt. Chase learns that Brooke cheated on her calculus exam, while nudity and drugs run rampant in the halls of the school.
Haley confronts Brooke regarding the stolen calculus test. Lucas and Peyton consider taking their relationship to the next level as Peyton and Brooke grow closer. In Deb's absence, Nathan throws a senior party at the Scott House, where a sex tape from Nathan's past surfaces.
On the day of Prom, the residue of Nathan's pre-Prom party has serious repercussions for everyone in Tree Hill. Haley asks Nathan for a list of his past sexual conquests. Rachel is suspended after taking the blame for the exam she stole with Brooke. Peyton tells Lucas she wants to skip the Prom entirely, but he refuses to take no for an answer. Finally Mouth and Brooke must deal with dating Clean Teens on Prom night.
It will be an unforgettable Prom at Tree Hill High when Lucas discovers who was in the hallway when Keith was killed. Meanwhile, Peyton's decision to skip Prom leads to dire consequences. Nathan and Haley vow to be romantic teenagers at Prom, while Dan tries to win Karen's affections, as the witness to his murder closes in.
Skills finds Lucas sleeping besides Peyton and Brooke who made up and felt scared alone after fighting fake Derek. When they get a message from Mouth he's in trouble, they all decide to go together as a road-trip, and drive on taking turns. After sleeping in a small-town park, 'vagrant' Mouth is in jail, where a giant biker type who recognizes him from Brooke's fashion show protects him, till he makes friends with all jailbirds. On the back-road they took in Texas to see the Elvis-shaped sandwich, their car breaks down and Chris Keller's tour-bus driving by stops and ...
Nathan and Haley grow closer in spite of the recent scandal. Brooke wonders if a spark might be rekindled with Chase. Peyton receives a tempting offer that would ultimately take her away from Tree Hill. Mouth reconnects with Gigi, while Lucas tells Karen that Dan is a murderer, setting off an explosive series of events.
As graduation day dawns in Tree Hill, some dreams begin as others end. Haley prepares for her graduation speech and her role as a young mother, while Nathan prepares for life without basketball. Brooke makes a heartfelt confession that puts her future in jeopardy. Lucas confronts Dan as Karen's life is threatened.
Haley gives birth to Nathan's son: James 'Jamie' Lucas Scott. After Karen nearly dies having her and Keith's daughter Lily, Dan confesses Keith's murder and goes to prison. Two weeks later, Deb babysits when Rachel hosts a nostalgic graduation class exit party. Chase and Lucas insist Brooke and Peyton try their career opportunities before returning to them. The Scott brothers gather the courage to visit dad, Dan, in jail, then decide against it, while he fails trying to hang himself. Lucas accepts becoming Jamie's godfather and Coach Whitey's college assistant.