Tree Hill bids goodbye to the past while anticipating the future: Lucas and Peyton prepare for the birth of their child with the help of a surprise visitor, Dan nears his end, and Brooke works with Victoria to relaunch Clothes Over Bro's. Meanwhile, Nathan returns to Tree Hill to face Haley and Jamie after being released from the Chiefs.
The families of Tree Hill draw closer as Lucas bonds with Jamie while working on Peyton's car, Sam develops a connection with Victoria, and Brooke and Haley throw Peyton a baby shower. Meanwhile, Nathan's ambitions seem closer than ever when he learns that an NBA scout will be watching his next game.
The parents of Tree Hill face difficult challenges: Lucas finds himself fighting to stay calm when Peyton's pregnancy faces further problems, Nathan and Haley clash over the decision to pull Jamie out of school, and Victoria returns to tempt Brooke back into the business. Meanwhile, Mouth continues to mend his relationship with Millie.
As Lucas begins to start casting for his movie, Peyton begins to put together plans for their wedding. Meanwhile, Dan gives Jamie advise when he has his first school crush; Brooke is introduced to the actress that will play her in Lucas' movie; Nathan receives exciting news; and Haley is forced to make a tough decision at work.
Brooke is shocked to find out that Samantha is in her room with a boy named Jack. Along with that, Julian asks her to make some clothes for the movie. Peyton tries to get Mia to focus on her follow-up album. Lucas is excited when he travels to Hollywood to meet the director of the movie. Meanwhile, Nathan gets the chance for a pro-basketball try-out. Haley takes Jamie to his school's talent show and Millicent confronts Mouth about Gigi.
Lucas falls asleep and dreams of a 1940s Tree Hill were he owns Karen's Cafe. Here, Dan is a dangerous mobster and everyone is entangled in his web: Brooke owes him money, Mouth is searching for proof that would link him to Keith's murder, Haley is his former lounge singer, and Lucas is in love with his step-daughter Peyton.
Tension arises backstage at Peyton's USO show as Lucas deals with Peyton and Julian's past. While Haley tries to find a way to ease her stage fright, Nathan grapples with a decision that could forever change his career. Meanwhile, Brooke receives a call that could end her relationship with Sam and Millicent confronts Mouth over Gigi.
Lucas' novel receives interest from a suprising person, as does Mouth as he meets his new intern. Jamie begins to develop a crush on Sam and her rebellious ways, while someone becomes enamored with Brooke. Meanwhile, Haley and Nathan discuss his return to baskeball as his comeback begins to look more like a reality.
As Lucas sets out on his book tour, he runs into a person from his past. Nathan finally gets a chance to prove himself on the court, but begins to question his health as he does so. Meanwhile, Haley reaches out to a student; Brooke debates a life-changing decision; and Peyton confronts Mick over his true identity.
Tree Hill residents are surprised to learn that a couple will indeed get married. Brooke tries to adjust to life after the robbery at "Clothes Over Bros". Nathan and Haley receive devastating news and Nanny Carrie's return creates more blanks than answers, after she kidnaps Dan - whose life is in jeopardy.
In the sixth season premiere, Tree Hill residents must make a decision that will change their lives forever. Lucas finally pursues his dream with the woman he loves, Brooke must face a reunion with her mother, Mouth makes a revelation, Nathan and Haley must face a ghost from their past and the news of Dan's accident is slowly beginning to spread.