When someone unleashes the students' time capsule upon Tree Hill High, 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. Haley is forced to reconcile the man Nathan was before with the man he has become, and Peyton's Breast Cancer Benefit Concert at Tric features performances by Haley, Jack's Mannequin and the return of Fall Out Boy.

The aftermath of the school shooting and the death of Jimmy Edwards forces everyone in 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, while Lucas and Peyton consider the implications of their kiss in the library.

Nathan worries about Haley as they prepare to renew their vows. Peyton and Brooke's friendship becomes strained and Deb confesses to Dan about the fire.

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.

Peyton spends more time getting to know her newfound brother, Derek. Meanwhile, Lucas gives up on his love for Brooke and Rachel tries to start a romance with Nathan.