Dan must face the harsh consequences of his decision to murder Keith as Karen and Haley's pregnancies complicate the lives of Nathan and the graduating seniors of Tree Hill High. Lucas wrestles with his post-high school options, and Peyton and Brooke prepare to spend the summer in Los Angeles together.
As the end of the school year approaches, Peyton considers participating in a music internship in Los Angeles, while Brooke tries to reconnect with Chase through yearbook signatures, and Haley struggles to write her valedictorian speech. Meanwhile, Dan suggests that Lucas get professional help when Karen worries about his obsession with theories about Keith's murder.
When Mouth and Rachel's road trip goes wrong, the other teens go out to their rescue. While on the trip, Nathan and Haley get a second chance to enjoy their Prom and Peyton and Lucas decide to take their relationship to the next level. Finally, Brooke reveals the truth about the stolen calculus exam to Haley.
It's Prom night, but things start to go awry as Lucas discovers who was the person in the hallway when Keith was killed, and psycho Derek holds Peyton hostage at her own house. Meanwhile, Haley and Nathan vow to be romantic with each other throughout the night, and Dan continues to win over Karen's affections.
It's Prom day, and emotions are flying high at Tree Hill. An emotional Haley confronts Nathan about the sex tape and asks for a list of all his past sexual encounters. Meanwhile, an angry Peyton asks Lucas to skip the dance altogether, but he refuses to take no for an answer. Finally, Brooke and Peyton let out all their tension in a confrontation that can tear them apart forever.
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.
The aftermath of the series of unfortunate events at Tree Hill begins. Lucas returns to his everyday life, following his heart attack, and tries to rekindle his relationship with Peyton. However, things are rougher for Haley when she discovers that Nathan had more involvement in her accident than she could have ever imagined.
Nathan struggles with money problems and reluctantly asks Dan for help. Elsewhere Brooke learns the new man in her life is also her new English teacher. Peyton gets help from an unexpected source, and Lucas returns to the Ravens just in time to help the team advance in the playoffs for the state championship.
The residents of Tree Hill must deal with the aftermath of the shocking accident that left everyone without words. In the midst of all the chaos, Dan extends his help to Karen now that she is pregnant, Lucas and Peyton's friendship continues to grow stronger, and once rivals Brooke and Rachel move past their differences and manage to become good friends. Brooke has a difficult decision to make about her relationship with Lucas and Skills decides to try out for the Ravens.