Set in the fictional North Carolina coastal town of Tree Hill, the main storyline in the early seasons is the relationship between two half-brothers, Lucas and Nathan Scott, who start out as enemies but bond as the show progresses. In the pilot episode, Lucas becomes a member of the Tree Hill Ravens (the high school basketball team) with the help of his uncle Keith. Nathan, already the head of the team, is threatened by this and it becomes the basis of their rivalry, also fueled by Lucas's romantic interest in Nathan's girlfriend Peyton Sawyer. Later on, Brooke Davis, Peyton's best friend, tries to date Lucas, while Nathan attempts to date Lucas's best friend Haley James. The character of Lucas and Nathan's father Dan Scott is occasionally explored throughout, including his relationships with Karen Roe, Lucas's mother, and Deb Scott, Nathan's mother, and how he ended up with one woman rather than the other, thus abandoning Lucas as his son.
The first season deals with the first half of the main teenage characters' junior year. The focus is on the rivalry between Lucas and Nathan during the basketball season. 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.
The second season focuses on the second half of the characters' junior year. It sets aside basketball and explores new romances and characters. Lucas dates Anna Taggaro, Peyton dates Jake Jagielski, and there is a love triangle between Brooke, Felix Taggaro, and Mouth McFadden. This season also shows the strain on Nathan and Haley's relationship because of Chris Keller, and the repercussions – especially for Lucas – of Dan's hypertrophic cardiomyopathy, an inherited disease. Haley's decision to go on a music tour with Keller causes Nathan to file for divorce. Peyton deals with drug problems and the return of her biological mother, and Karen opens a nightclub and begins a relationship with a professor. A troubled Deb struggles with drug addiction. The end of the season sees Nathan go off to High Flyers, an all-star basketball camp, as Haley tries to reconcile with him.
The third season focuses on the characters' first half of their senior year, and also has the return of basketball. It features the arrival of Rachel Gatina, who brings conflict between Brooke and Lucas. Peyton deals with the return of her mom, Ellie, and tries to get to know her when she finds out she is dying from cancer. Jake and Peyton's relationship draws to a close and Peyton's romantic feelings for Lucas resurface later in the season. The later episodes of the season see Nathan and Haley plan their wedding. 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, Peyton getting shot in the leg, Jimmy Edwards committing suicide and Dan murdering Keith. At the end of the season finale, after Nathan and Haley renew their vows, he, Rachel, and Cooper are left fighting for their lives after a car accident.
The fourth season features the second half of the characters' senior year, and predominantly, the love triangle of Peyton, Lucas, and Brooke. Haley finds out she is pregnant, but the news is threatened by Nathan's risky forays into gambling and loan sharks. Peyton is stalked by an impostor posing as her half-brother. 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. Brooke explores a romantic relationship with Chase Adams and a close friendship with Rachel. The season ends with the group's graduation from high school, Lucas discovering that Dan killed Keith, and Haley and Karen having their babies.
The fifth season jumps four years into the future. The characters struggle with adulthood after college and eventually return to Tree Hill for various reasons. Lucas, now a published author, is in a committed relationship with his editor, Lindsey Strauss, which turns into a love triangle when Peyton returns after a failed music production career in Los Angeles. The marriage of Nathan and Haley goes into crisis as Nathan faces major depression after being seriously injured the night he was drafted into the NBA, and a stalker nanny, who is in love with Nathan, moves in. Brooke looks for life beyond success in her work and struggles to get acceptance from her mother Victoria. Lucas and Skills return to the Tree Hill Ravens as coaches and ask for Nathan's help with star player Quentin. Mouth begins a relationship with his boss Alice, to get ahead in his job, but later settles down with Brooke's assistant, Millicent Huxtable.
The sixth season features the progression of Peyton's romance with Lucas as they reunite and deal with her dangerous pregnancy. Peyton also meets her birth father, Lucas's book is optioned for a feature film by Peyton's ex-boyfriend, producer Julian Baker, and Nathan and Haley struggle to reach their dreams after being terrorized by Nanny Carrie who tried to kidnap their son Jamie. Brooke is attacked in her store, leaving her scarred mentally. She later takes in a foster child. Mouth and Millicent's relationship hits the rocks when Mouth's ex returns. And a seriously ill Dan comes to terms with his life and how much time he has left. Brooke enters a relationship with Julian.
The seventh season jumps fourteen months ahead. Lucas and Peyton have moved away. Rachel returns and two new regular characters are introduced: Haley's sister Quinn and Nathan's agent Clay, and their relationship develops after the death of Clay's wife. Nathan's NBA career is jeopardized by a cheating scandal that also affects his marriage with Haley. Brooke releases her new clothing line in the midst of conflicts with Julian and Alex, a model she hired for her company. Millicent struggles with a drug addiction which causes Mouth to break up with her. The second half of the season deals with Haley's depression due to her mother's death. At the end of the season, the characters travel to Utah for the premiere of Julian's completed film, Haley announces she's pregnant again, Julian proposes to Brooke, and Clay and Quinn are shot.
The eighth season mostly centers around the wedding of Brooke and Julian, Haley and Nathan's pregnancy, Clay and Quinn surviving their life-threatening attack, and Brooke losing her company. Mia returns and the romance between Alex and Chase turns into a love triangle, while Mouth and Millicent reconcile. Nathan returns to college but struggles to fit in so Nathan and Clay start a sports management company named Fortitude. A fierce storm reaches Tree Hill, endangering the lives of Brooke and Jamie. Brooke and Julian look into adoption and are connected to a pregnant teen who later decides to keep her baby, leaving Brooke heartbroken. Meanwhile, Haley gives birth to a baby girl and names her Lydia (after Haley's mother). Alex and Chase finally get together. Brooke becomes pregnant and has twins.
The ninth and final season mainly focuses on the kidnapping of Nathan, while Haley faces multiple problems running the new Karen's Cafe. Brooke and Julian adjust to life as parents, which leads Julian to make a life-changing mistake. A mysterious problem haunts Clay and he ends up in psychiatric care, where he meets his son, Logan, with the support of Quinn. Millicent is forced to deal with Mouth's sudden weight gain, and Chase starts a friendship with Chris Keller. Lucas returns to Tree Hill as Haley reaches out to him for help. Nathan is later found alive with the help of Dan before he passes away. The series ends as Tric celebrates its tenth anniversary while the entire Tree Hill family (except Lucas and Peyton) face new and exciting possibilities for their futures. Jamie Scott is now a teenager and is the Ravens' new shooting guard.