In the third season premiere, we finally discover Dan's fate after the fire. Besides the situation with his father, Nathan also has to deal with Haley's reappearance in Tree Hill and the future of their relationship. Meanwhile, Peyton tries to find the truth about the mysterious woman who pretends to be her mother. Also, Lucas looks forward to Brooke's return after a summer apart.

Brooke has an end of the summer party on the beach. As Nathan comes home from basketball camp, Haley tries to tell him how she feels. Elsewhere Lucas deals with Brooke's rules for dating and Peyton deals with family issues.

Nathan asks Haley for a possible divorce. Lucas tells Dan that he saved his life. Peyton finds out something deep about Ellie. Dan tries to drop accusations at several people about the fire. He also tries to get Whitey replaced as Ravens coach.

It's Halloween in Tree Hill and everybody is celebrating at Tric, with special guest band Fall Out Boy. The masquerade ball gives the opportunity to Haley to win back Nathan while Brooke is trying to seduce Lucas. Also, Peyton decides to face her new mother and get to know her; Dan uses blackmail to become mayor but things don't turn out as easy as he thought they would when Deb gets in his way.

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.

Lucas attempts to play in the first game after Keith's death, but cannot bring himself to do it; Nathan and Haley prepare to renew their vows, while Mouth tries to get closer to Rachel; Peyton receives a surprising offer; and Brooke finds a way to get revenge on Rachel.