Other major storylines are Nathan and Haley's developing relationship, the Peyton-Lucas-Brooke love triangle, and the love quadrangle involving Lucas and Nathan's parents.
It sets aside basketball and explores new romances and characters.
Lucas dates Anna Taggaro, Jake Jagielski dates Peyton, and there is a love triangle between Felix Taggaro, Brooke and Mouth Mc Fadden.
A major subplot consists of Dan's efforts to solve the murder attempt that was made against him during the previous season's cliffhanger.
A major episode ("With Tired Eyes, Tired Minds, Tired Souls, We Slept") involves most of the main cast in a hostage situation at Tree Hill High and culminates in Peyton getting shot in the leg, Jimmy Edwards committing suicide and Dan murdering Keith.
This season also shows the disintegration of Nathan and Haley's relationship because of Chris Keller, and the repercussions – especially for Lucas – of Dan's hypertrophic cardiomyopathy, an inherited disease.
Peyton deals with drug problems and the return of her biological mother, and Karen opens a nightclub and begins a relationship with professor. The third season focuses on the characters' first half of their senior year, and also has the return of basketball.
Lucas looks for the truth behind his uncle's death as he documents his life since joining the Ravens basketball team.
Lucas and Peyton enter into an official relationship after the Ravens win the state championship, while Dan rekindles his romance with Karen, much to Lucas's dismay.
It features the arrival of Rachel Gatina, who brings conflict between Brooke and Lucas.