Dan is found alive outside the dealership. Nathan, still mad at Haley, tells her he's leaving for camp, while she would make amends with him and continue their relationship. Lucas and Peyton come back home from the beach and tell each other it's always gonna be them, no matter what. Three months later, Karen and Brooke come back to town as Dan has recovered. Lucas and Peyton have spent the whole summer together, forming a great friendship and making their bond stronger than ever. Peyton feels like her mother lied to her by not telling her she was adopted: Larry reassures her they planned to but couldn't because she died. Brooke tells Lucas she's thought they could have a non-exclusive fling, being able to see other people: he hesitantly accepts, pretending to be satisfied although he would try again to be together with her for real. Deb tells Dan she wants to divorce. Brooke moves into Nathan's old apartment with Haley, whom Peyton is mad at for having left. Dan reveals he remembers seeing someone that night while passing out. Lucas tells Peyton Ellie is back in town. At camp, Nathan is still wearing his wedding ring as a necklace.

Brooke throws a beach party to celebrate the end of the last summer before graduation. Nathan returns to town and wants nothing to do with Lucas or talk to Haley. Peyton learns from Ellie she tried to visit her when she was ten and Larry hid it from her. Dan has been having flashbacks from the night of the fire and confronts Karen about who could have tried to kill him. Lucas spots Ellie in town seemingly making a drug deal, then, at the party, he tells Peyton what he saw. Lucas confronts Nathan and says he can hate him, but if he hurts Haley he will hurt him, causing him to show up to the beach and tell Haley he doesn't want to hurt her, but he's just not ready to figure out what they are now to each other yet. Lucas tells Brooke, who is flirting with other guys, he's the guy for her and one day she will realize it. Peyton confronts Ellie about the drugs. Dan comes to the beach, and seeing Lucas by the bonfire triggers a memory from the night of the fire, in which he remembers Lucas in the dealership.

Lucas and Haley meet on the roof of the cafe and remember all that happened in the last year as they agree to write their new yearly predictions after having seen how the first day of school goes. As senior year begins, Haley and Nathan awkwardly avoid each other. Ellie tells Lucas she was buying marijuana because she has cancer: she didn't tell Peyton because she wanted to know her on her own terms. Dan confronts Lucas about being in the dealership, but he denies it, and Dan warns him it's not over. Larry lets Ellie visit Peyton's room which upsets her who sees it as an invasion of privacy. Brooke gets a job at a clothes store. Peyton and Lucas talk in the gym: he tells her about Ellie's diagnosis. Dan arrives and nearly strangles Lucas thinking it was him who tried to kill him, so Peyton reveals Lucas actually is the one who saved his life that night. Nathan tells Haley he wants a divorce, but before that he wants them to be apart for a year to see what happens in the meantime: Haley tells him she knows they will be together.

Peyton and Brooke throw a costume party at Tric. Lucas wants to wear something to make Brooke commit to him. Due to advice for Brooke, Haley tries to seduce Nathan in order to get him back. Peyton struggles with the decision of having a relationship with Ellie or not, especially after finding out that Ellie likes the same music she does, something she thought she got from her mom. Dan announces he's running for Mayor to Deb, telling her he won't give her the divorce until the race is over, so they must keep up appearances. Nathan still isn't ready to talk to Haley, even though Brooke thinks they can reunite at the party, where Lucas meets a new girl who flirts with him, making Brooke jealous. Later that night, Nathan meets with Chris Keller and asks him to help Haley with her music as she's been having writing block. Larry advises Peyton to talk to Ellie, saying she is lucky she has the time to get to know her as she didn't have the time to know her mother would die. Ellie is seen drawing a picture of Peyton, revealing that Peyton also got the talent from her.

Dan is announcing his run for Mayor at the Midnight Madness basketball game, when they will retire his jersey. Peyton learns Ellie has been writing about meeting her and that she is an artist, which makes her furious, telling her to leave town. At the game, Karen surprises Dan announcing her run for Mayor too. Lucas grows tired of Nathan ignoring Haley leading them to have a fight on the court: furious, Whitey makes the two co-captains of the team. Brooke has a fight with a new cheerleader, Rachel Gatina, who is trying to steal her the spotlight and is also the girl whom Lucas met at the party: Rachel, viewing Brooke as a competition, flirts with Lucas to bother her. Unfortunately, Brooke inadvertently sets Lucas up with her due to the non-exclusive thing, because of which she and Lucas argue too as they really cannot get each other. Nathan tells Haley if she can work with Chris and feel nothing towards him, maybe they can be together again, so she accepts Chris' offer to make music with him again.

When the cheerleaders start fighting over the same guys, Brooke throws a "Fantasy Boy Draft". Haley and Peyton argue about how the first behaved with Nathan. Haley and Chris work on her music, which is only good when she writes about Nathan. Trying to keep his heart condition a secret, Lucas struggles to be physically fit enough to play, while Haley realizes he hasn't told Whitey about his HCM, so she warns him to do so, but Lucas says if Whitey discovered the truth about his disease, he would prevent him from continuing to play: Lucas promises to be careful, taking his medication. At the draft, Peyton surprisingly picks Mouth, Brooke picks Chris Keller, while Rachel picks Lucas to bother Brooke and Haley picks Nathan: shocked, Brooke realizes it happenened the thing she least wanted to happen. Haley thanks Peyton for not picking Nathan, but Peyton says it was about time she started fighting for her husband. Lucas struggles with his basketball training as his medication weakens him. Karen and Deb organize a move to humiliate Dan as Brooke fills in the slots for her draft, with Rachel getting Lucas. Peyton feels bad for sending Ellie away.

The night of the Fantasy Date Draft, Haley is upset of having to double date with Chris and Brooke as she wanted a private date alone with Nathan. The night fails to bring Haley and Nathan closer together. During their date, Rachel would Lucas to forget Brooke, telling him she is very skeptical about her being the one for him, especially considering that until recently he felt that way about Peyton, but he stubbornly sticks to his idea. Karen and Deb vandalize Dan's billboard, but the night does not go as planned. Peyton and Mouth spend their date visiting Mouth's grandfather who has dementia and cannot remember his family. Haley brings Nathan up to the cafe roof and shows him the prediction she made as he writes one of his own, making her promise not to read it until the end of the year. Lucas goes to Brooke's apartment because he would be with her and walks into her room, seeing her waking up and, as she turns around, Chris rolls over, meaning the they have slept together: Lucas is disgusted by the vision and furious at Brooke.

Lucas, mad at Brooke for sleeping with Keller, refuses to answer her calls. Karen does a radio interview for the election, but Dan ambushes it by calling her and asking unflattering questions. Peyton is there for Lucas in his time of emotional pain. Dan threatens Lucas to tell Whitey about his HCM if he does not pass the ball to Nathan and sit out for the season. In the locker room before a game, Lucas and Nathan begin arguing again. Peyton gives Haley a ride to the game and tells her she is sick of everyone leaving and that is the reason she has been mad at her, but then adds that she is happy she is home: the two finally make amends. The Ravens lose the game. Dan comes in and berates the team. Nathan starts to back talk to him, who pins Nathan up against the wall just as Whitey walks in telling him to get out. After the game, Lucas ignores Brooke, while Haley waits for Nathan, who tells her he wants to walk home alone, but then he asks her to go with him. Lucas stops at the river and angrily throws away his medication.

After stealing Brooke's clothes from the store selling her designs, Brooke, Peyton, and Haley find themselves behind bars. Lucas confronts Brooke about her cheating: she apologizes, but he says that she has made it clear she does not care about him. Peyton is annoyed by the presence of her guilty conscience after losing Ellie's cancer survivor bracelet. Dan wins the election while Lucas meets with Deb, who is revealed to be the one who tried to kill Dan: Lucas warns her that Dan will not rest until he punishes someone, so she leaves Tree Hill. Nathan finds Haley and tells her that he misses having her with him when life gets rough and asks her if she wants to stay the night, at which Haley happily accepts: the two sleep together for the first time since she got back home. Peyton finds Ellie's address. Brooke finds Lucas and confesses that she wrote him a letter every day during the summer but never sent them because she was afraid to get hurt again and apologizes once more: Lucas decides to forgive her, so the two get back together and start dating exclusively.

Lucas and Peyton take a road trip together to find Ellie. Brooke tries to trust Lucas and Peyton, but the image of what happened the year before resurface in her head, so she becomes jealous again. While out of town, Lucas reconnects with a friend from the past, Faith. Deb and Nathan have a talk which leads to secrets being revealed. Brooke, Haley and Mouth successfully launch the Clothes Over Bros' website, only to find that demand far exceeds supply. Peyton shows up to Ellie's house and asks for help with Haley's record and asks about her cancer status.

The Ravens lose their second game in a row, which leads Whitey to try some very tough love. Dan implants a thought about Haley in Nathan's head which leads him to think it is true. After being gone for six months, Keith returns and reconnects with Lucas and Karen. Brooke receives a mysterious letter inviting her to a fashion showcase. Keith and Karen reconnect and when he asks her about Andy, she replies that he was not the man for her. Peyton and Ellie keep deepening their relationship, bonding over their common passion for music. Feeling they have a very weak emotional connection, Brooke and Lucas decide to start writing each other some letters, like she did for him during the summer, to get to know one another better.

The students meet with the school counselor. Nathan and Haley realize they want to attend colleges which are thousands of miles away from one another. Keith is questioned by the police for the fire, but cannot be held as they have no evidence, then he asks Karen out on their first date to the Ravens game. Peyton talks with Ellie about college, and Ellie says she could see her studying art, music, or maybe business. At the game, Whitey forces Nathan to sit out the game. During the last few seconds of the game, Nathan talks to Lucas and reminds him to put the ball in the dead spot. Lucas takes his advice and the Ravens win the game. Flashbacks to the counseling session show Brooke revealing she does not like to talk about college because she will be alone, while Peyton says she now wants to maybe study art, music, or business, as Ellie has advised. At home, Ellie shows Peyton an idea for a CD called "Friends With Benefit". Keith, Karen, and Lucas enjoy a meal while Dan watches from outside: Keith tells him to go home as he is not in their life.

A violent rainstorm hits Tree Hill, causing a blackout. Lucas and Brooke, stuck together in her apartment, begin arguing again due to a letter he wrote her using the exact same words he had used the year before in one for Peyton, leading the two to have a fight out in the downpour. Nathan and Haley, who are at Nathan's home, have a serious conversation about their issues and reconcile once and for all, promising to never be separated again. Peyton shares some intimate moments with Ellie, revealing she is scared of her not surviving cancer, but Ellie tries to reassure her and then tells Peyton she has to stop being afraid and to begin living rather than surviving. Peyton, inspired by her words, talks about how she loved Lucas but let him go, regretting it and fearing she has made an irreversible mistake: Ellie tells her it is never too late. Keith and Karen are at the cafe and finally give in to their feelings and make love for the first time. The day after, Peyton goes to see Ellie, but she is shocked and devastated to find her dead.

Peyton and Haley take a road trip to New York with Brooke for the fashion show, but after one night in the city, Brooke comes to a realization. The basketball team and cheerleaders road trip to the cheer competition. After returning to NC, after a night of drinking, Peyton and Lucas find each other in the same bed, while their bond keeps growing stronger and stronger. Nathan and Lucas go to dinner with Tony Battle, an old friend of Nathan. Peyton gets drunk with Rachel, and because of the room swaps she stays with Lucas. Karen considers an impromptu marriage proposal to Keith.

Clips of the students' time capsule from Junior year are leaked and played on the TVs all over school. This results in embarrassment for many of the Tree Hill gang, but also a reconnection in old friends. Peyton flirts with Fall Out Boy songwriter Pete Wentz. Keith gives Lucas an option of a lifetime. The concert features performances by Haley, Fall Out Boy, and Jack's Mannequin. The show references Jack's Mannequin singer, Andrew McMahon, and his real life battle with leukemia.

Jimmy Edwards, an outcast and bullied student at Tree Hill High, down and depressed after the leaking of the time capsule, goes to school with a gun and, after yet more abuse, begins shooting, hitting Peyton in the leg and causing panic. The school is put in lockdown while Jimmy takes Haley and other students hostage. Outside the school, Brooke is desperate because she has lost Peyton in the crowd and tells Lucas, so he and Nathan rush into the school to save Peyton and Haley respectively. Lucas finds Peyton wounded in the library and stays with her, promising that nothing will happen to her. Believing she will not survive because of the blood loss, she finally confesses she loves him and the two share a brief but meaningful kiss, then she passes out and Lucas decides to risk it all, taking her in his arms and trying to exit the school. Jimmy finds them and threatens them. Keith gets into the building and assists Lucas and Peyton in escaping by trying to calm Jimmy, who, feeling too guilty about what he has done, shoots himself. Then Dan arrives, collects Jimmy's gun from the ground and shoots Keith, killing him.

Two weeks have passed. Peyton has recovered from her injury, Lucas and Karen, both devasted, are mourning Keith and everyone is still traumatized. Brooke, convinced it will give a feeling of normality, throws a party at school to Lucas' anger, who thinks it is only disrespectful for Keith: the two have yet another fight, during which he even tells her she can't understand the situation because she was not there. Both Lucas and Peyton are still thinking about what happened between them and they meet again in the library, sharing another intimate moment: they decide to pretend it meant nothing and it was only because of the situation not to hurt Brooke. Besides, Lucas is able to find some peace from his pain only being around Peyton. Nathan and Haley agree they're lucky of having what they have together, because it could vanish in a moment, like it happened with Keith's life. Brooke, more and more aware that Lucas and Peyton's bond is still too strong to be platonic, tells Peyton it's obvious the two of them love each other and they both know it's true: Peyton, feeling once again guilty, is forced to lie to her about the truth.

Karen is still desperate for Keith's death. Trying to recover from the late tragic events, the gang decide to go away from Tree hill to spend a weekend in the mountains in Rachel's cabin. Nathan, feeling that life is too short, proposes again to Haley, who happily accepts. Brooke discovers some important details about Rachel's past, while Peyton decides to start a fling with Pete Wentz, an older musician she has recently met.

Seeing how devastating Keith's death has been for Karen and understanding how important life is to put it at risk, Lucas decides to tell her, Whitey and Nathan the truth about his heart condition and then painfully quits the team because continuing to play is too dangerous, seeing his dream of becoming a professional player vanishing. He and Brooke keep growing more and more emotionally distant. Nathan and Haley begin organizing their wedding, while Brooke uses what she's discovered at the cabin to take revenge on Rachel. Peyton is still messed up due to the last traumatic events and asks her father Larry advice about what to do regarding her love life after ending her fling with Pete. Larry's words prompt her to make a decision: she goes to Savannah to find Jake, thinking it could be what her heart wants.

Lucas and Karen have gone away from Tree Hill for some days to recover from the last traumatic events and to make him visit some colleges he would like to attend. During the playoff night for the Ravens, with Lucas gone, Nathan has to lead the team to the win alone. Peyton is spending some time in Savannah with Jake and the two rekindle their relationship: feeling safe with him and Jenny and thinking it could be enough to be happy, she decides to stay and proposes to him.

Jake accepts Peyton's proposal, but then hears her saying in her sleep she loves Lucas. After talking about what happened the day of the shooting, he realizes she's just running away from her true feelings, trying to bury them not to hurt Brooke due to her and Lucas still dating: he tells her she needs to get back home and clear her mind about who she truly loves. Lucas comes back too, after having realized he wants to become a writer. Brooke organizes a sort of comic show at Nathan and Haley's rehearsal dinner to relive their love story while she has also realized, with him being away, that she feels better without Lucas and she hasn't even missed him, understanding she is not so dependent on him. During the show, Lucas and Peyton are very nervous to play Nathan and Haley proclaiming their love to each other: while doing the scene, Peyton flashbacks to all the journey of her and Lucas' relationship from the very beginning as she finally realizes he's the one for her and she is still in love with him. At the end of the night, she decides to tell a shocked Brooke the truth.

It's Nathan and Haley's wedding day. After Peyton's confession, she and Brooke have a huge argument, ending their friendship again. At the wedding, Lucas lets it slip with Brooke about the kiss with Peyton, thinking she already knew, leading to yet another fight. The two begin throwing at each other all the lacks in their relationship: Lucas tries to justify himself for the kiss, explaining in which situation it happened and reminding Brooke how he forgave her for sleeping with Keller, thus thinking her anger towards him is unfair, as she responds that a kiss always means something, no matter in which situation it happens, and that the "I love you's" only said in words but not supported by facts, as it is between them two, have no meaning at all, since they only push each other away and feel better when they are apart, which is the exact opposite of what a couple should be. The two remain at odds and have certainly reached their worst moment. Karen tells Lucas she is pregnant with Keith's child. After the wedding, Nathan and Haley leave for the honeymoon, but they have a car crash.