Season One
When Lucas joins the Ravens, Nathan is not happy, especially at the growing attraction between his girlfriend, Peyton Sawyer and Lucas. Encouraged by Dan, Nathan makes life on the team difficult for Lucas and turns the other players (bar Jake Jagielski) against him. However, Nathan later decides on a more subtle way to get at Lucas and he convinces Lucas' best friend Haley James to tutor him as Nathan is failing in most classes. Nathan intends to use Haley as a tool in his destruction of Lucas but when Peyton dumps Nathan for his attitude, Nathan opens up with Haley and they become close. Naturally, Lucas is unhappy when he hears that Haley is tutoring Nathan but he realizes that there is nothing he can do to stop it. Nathan and Haley become a couple and he turns to her as his situation at home becomes worse. Nathan is now Haley's boyfriend and he is adjusting to having a serious relationship and his personality changes when Haley is his girlfriend. Dan has little faith in Nathan and is constantly belittling him, pushing Nathan to breaking point. Nathan takes amphetamines to enhance his performance and beat Dan's scoring record but this backfires and Nathan's attitude changes and he tries to get Haley to have sex with him and ends up in hospital after collapsing on the court. Nathan tells Haley that he was thinking about her when he collapsed and they kiss and he tells her that he will wait until she is ready to have sex. Nathan and Haley take off a day of class and spend time together on the beach. Dan and Deb separate after this and later Deb files for divorce. Nathan is caught in the middle and when Deb admits to having an affair in the past, Nathan decides he wants nothing more to do with either parent and is granted emancipation from them. Nathan moves into his own apartment and gets a job at a pretzel counter. When Whitey takes time off from coaching to have eye surgery, Dan takes over the reigns as coach and makes life difficult for both Nathan and Lucas. However, the two brothers are surprised to find themselves actually getting along and they form a united front against their father. Meanwhile, Nathan struggles to accept Haley's decision to wait until she is ready to have sex. Nathan and Haley realise they are in love with each other but Haley is disheartened when she finds porn on Nathan's computer as well as pictures of Peyton. Nathan convinces Haley to give their relationship another go and she agrees to sleep with him. The Ravens lose the Playoffs and Nathan and Lucas part on good terms as Lucas prepares to move to Charleston with Keith. When Lucas comes to Nathan's apartment to say goodbye to Haley, they tell him that they got married the night before.


Season Two
The next day, Nathan and Haley learn that Dan has had a heart attack. At the hospital, they tell Deb of their marriage but she is surprisingly angry and refuses to accept it, nor does Dan when he wakes up. Lucas and Keith return to Tree Hill and Lucas, Peyton and Brooke throw Nathan and Haley a wedding reception while Keith, filling in for Dan at the dealership, takes Nathan on as a mechanic. Haley starts to blossom as a musician but Nathan is jealous of her closeness to fellow musician Chris Keller and warns Chris to stay away from Haley. When Haley's older sister Taylor James comes to Tree Hill, Nathan realises that Taylor is the girl to whom he lost his virginity several years ago before he had even known Haley. He and Haley fall out about this but later make up. When Haley mentions that Chris wants her to accompany him on tour, Nathan asks her if she kissed him and she finally admits it. Nathan tells his wife to choose between him and the tour. Haley chooses the tour and leaves Tree Hill. Nathan is devastated and goes on a downward spiral, drinking in class, punching his father and letting Lucas take the fall for his drunk-driving. Nathan finally gets his act together and goes to visit Haley in an attempt to get her to come home but this doesn't work out and he comes back to Tree Hill alone. When Nathan's uncle Cooper (Deb's brother and Nathan's role model) pays a visit to Tree Hill, he takes Nathan and Lucas to a racing track but tragedy strikes when Nathan attempts suicide by deliberately crashing the car. He ends up in hospital where he has a dream of what life would have been like if Dan had married Karen instead of Deb and Nathan and Lucas had grown up in each others' shoes. This dream makes Nathan realise how much he loves his mother. They agree to be strong for each other and Deb goes to rehab to overcome her pill addiction. Nathan decides to move home and Dan pays his medical bills in exchange for Nathan getting an annulment from Haley. Whitey offers Nathan the opportunity to go to "High Flyers", a prestigious basketball camp, for the summer but Dan tries to talk Nathan out of it, blaming him for Deb's addiction. When Deb learns of this, she and Nathan agree to leave Dan and make a fresh start. Nathan is annoyed that Lucas has been investigating Dan even though Nathan asked him not to. Nathan disowns his brother and moves back home with Deb. In the last episode(s), someone drugs Dan and sets fire to the dealership.


Season Three
(Continuing on the same night)Nathan goes to the door and there stands Haley. She returns to Tree Hill for good, but Nathan has not yet forgiven her or Lucas. Nathan learns that Haley is suffering musicians' block and pays Chris to come back to Tree Hill and help Haley with her music. Nathan and Haley grow close again and eventually get back together. Dan is crowned Mayor of Tree Hill and Deb tells Nathan that she started the dealership fire in an attempt to kill Dan; Nathan is angry with his mother and sends her away for a while to get her life in order. He patches things up with Lucas and when Jimmy Edwards brings a gun to school, Nathan races inside to find Haley. They are held hostage in the Tutor Center and the deaths of Edwards and Keith leave Nathan and Haley realizing that life is too short.


Nathan and Haley's wedding receptionThey move back in together and Nathan asks Haley to marry him again. While planning their (second) wedding, they receive a visit from Cooper but are dubious about his relationship with the younger Rachel. Deb returns and she and Nathan take out a restraining order against Dan while Nathan beats old "High Flyers" rival Damien West in an all-important game. On the morning of his wedding, Nathan is traumatised following a nightmare where Haley was drowning and he couldn't save her. He gets Lucas to keep a close eye on Haley but all goes well and they renew their vows, though Rachel causes a scene at the reception over Cooper sleeping with her despite her age. Nathan and Haley head to London for their honeymoon and Haley has something to tell Nathan but before he gets to hear it, they have a near-collision with Cooper and Rachel (in the wedding limo) on the Mollina Bridge. Nathan dives into the water to rescue his uncle but becomes trapped and is left gasping for air and fighting for his life.


Season Four
Nathan wakes up in hospital and is hailed as a hero for saving Rachel and Cooper. However, Nathan does not believe that he did save them - he thinks Keith did as he believes he saw Keith in the water. Rachel develops a crush on Nathan for saving her and sets out to seduce him, using his confusion over Keith to her advantage. Haley tells Nathan she is pregnant on the same day that he gets a scholarship to Duke University. He is initially annoyed that she kept it from him but is later delighted and tells Rachel that she never had a chance with him. Nathan and Haley face even more money difficulties now that they have a baby on the way and when Dan refuses to help, Nathan turns to a loan shark, Daunte Jones. He provides Nathan with money in exchange for Nathan losing the State Championship but when Haley learns that she and Nathan are having a boy, he decides not to lose for his son's sake. Afterwards, Daunte runs Haley down with his car and she ends up in hospital but both she and the baby pull through. Dan and Nathan believe that Nathan killed Daunte as he beat him up after he crashed. Dan takes the fall for Nathan but is released from prison when Daunte's autopsy results show that he was killed by the crash and not the beating. When Deb attempts suicide by taking an overdose, Nathan is racked with guilt. He and Haley decide to help Deb by moving out of their apartment and into the Scott Mansion. A party is thrown on the night before prom. A tape of Nathan's basketball glories is played but Nathan is horrified when it also reveals footage of him having sex with Brooke at a time when he and Peyton had just broken up for the 100th time. Haley asks Nathan to make a list of his conquests and Nathan tells Haley that she is the only one he loved. Haley forgives Nathan and they kiss and then go to the prom together. After Mouth sends a text saying he needs "ass", that is,'assistance', the gang goes to Honey Grove, Texas where Nathan and Haley have their dream prom. When they get back home, Nathan tells Lucas that an investigator has been calling him about point shaving and they are looking at Lucas. Lucas decides to take the fall after Haley ask him to. When Nathan finds out, he decides to come forward because he doesn't want to end up like Dan putting his future in front of everybody else. He holds a press conference and afterwards loses his scholarship. Nathan finds out from Deb that Dan killed Keith. When he confronts Dan about it, Dan doesn't deny it and Nathan disowns him and says he died the day Keith died. During graduation, Haley goes into labor in the middle of her valedictorian speech. Nathan stands up in happiness. Nathan and Haley soon welcome their son James Lucas Scott. Lucas and Nathan consider confronting Dan in jail, but agree that they will never do so. Nathan and Haley ask Lucas and Brooke to be James' godparents, which they happily accept.