Scott is having a hell of a night asking who those people back there were. Derek tells him they are hunters who have been hunting werewolves for centuries. Scott realizes he is cursed. Derek tells him the Bite is a gift. Scott retorts he doesn't want it. Derek tells Scott he needs Derek if he wants to learn how to control his shapeshifting. And so tells Scott he and Derek are brothers now. Derek heads off. The next morning Scott walks out in the woods. Stiles picks him up. Stiles reassures Scott they'll get through this new supernatural situation.
Scott apologizes to Allison for leaving her at the party. He hopes to get a second chance. Allison sees her dad and leaves. Suddenly, Scott sense of smell kicks in. Allison's dad is the leader of the hunters from the previous night.
Since Derek Hale is the only other werewolf Scott knows of, he believes that Derek is the one who bit him and is the murderer responsible for the girl in the woods. When Scott goes to the Hale House to confront Derek about talking to Allison, he smells human blood and spots a freshly dug grave. At night, Scott and Stiles dig up the other half of the body and get Derek arrested. They discover wolfsbane at the grave and learn on the ride back into town that proximity to it causes Scott pain and asthmatic-like symptoms. He seems unable to control his shifting, as well.
Scott ends up on a bowling date with Allison, Lydia, and Jackson, which is uncomfortable but gives Allison a chance to boost his self-esteem. Jackson reiterates his determination to find out Scott's secret. Scott takes Allison home. Stiles tells Scott the bus driver succumbed to his wounds and has died. Derek eventually convinces Scott that another werewolf, a more powerful, more animal Alpha, is responsible for Biting Scott, attacking the driver and committing the murders.
Despite the alpha murdering a video store clerk, Scott continues to try to distance himself from this new supernatural world. He wants to live a normal life and be with Allison. Derek insists that the Alpha will only give Scott until the next full moon to kill with him and join his pack. Derek says he's going to teach Scott how to control his abilities so he can help find the murderous Wolf. He gives Scott a rough time, breaking his arm justifying it will heal, to teach him that pain keeps him human.
Scott has to attend a parent-teacher conference as his grades are slipping because of the werewolf drama. Scott learns that it's Allison's birthday. Allison is embarrassed, but Scott gets she had to repeat a year because she moves around so much, which earns him a sweet kiss from Allison. Scott convinces Allison to play hooky. The two of them cut school and spend the day in the woods. Scott gets a call from Stiles who says Scott has to do something because of everything that's happening. Scott is perplexed at what he has to do. He and Allison tturn off their phones. Scott forgets that it's parent-teacher conference day, and he and Allison return too late for him to attend the meeting with his mom. During the commotion of the school parking lot, Chris Argent shoots a mountain lion which was the cause of the problem. Scott looks at the dead animal and realizes the seriousness of the situation.
Derek surprises Scott with a training session in a parking garage and warns him that Allison is a distraction but it turns out Allison is Scott's anchor. Stiles figures out that Allison calms him down, which helps him maintain control. The Alpha follows Scott and leaves a spiral in the frost on his car. Scott then has to save his boss, Alan Deaton, from Derek who believes he is the Alpha.
Scott decides that he's had enough of running from the Alpha and summons him instead. The Alpha werewolf immediately puts Derek out of commission and then toys with the teenagers. As a result of his manipulations, Scott, Allison, Stiles, Lydia and Jackson get trapped in the school with him. Scott believes it's his responsibility to try to get them out, so he goes to face the beast alone. The Alpha kills a janitor and then forces Scott to transform. While under the Alpha's thrall, Scott nearly kills his friends, but Allison's voice calls him back. Scott can't explain to her why he risked his life, so Allison breaks up with him because she can't trust him anymore.
Scott is heartbroken over his break up, which only intensifies the effects of the full moon. He hallucinate during a test at school and almost has a panic attack. Scott is made co-captain of the lacrosse team and lets Stiles know that he could smell the jealousy coming off Jackson. Stiles asks him to see if he can detect arousal on Lydia, and Scott ends up kissing her. Stiles feels betrayed and both punishes and tries to help Scott by handcuffing him to a radiator to keep him from killing anyone. Scott escapes and heads for Allison. He sees her and Jackson in a car together and hallucinates that they are kissing and tries to attack them. Derek appears from nowhere to stop him, and Scott surrenders when he realizes he's out of control. He begs Derek for a cure, and Derek tells him that the only one he's ever heard of is killing the alpha that Bit you.
Scott still believes he should be with Allison and tries reconnect with her, both for his emotional needs and because they need her pendant. Jackson figures out that Scott is a werewolf and threatens to expose him if he doesn't get Jackson the Bite as well. At a lacrosse game, Scott overhears the Argents discussing the possibility that one of the students might be a werewolf and realizes they think it's Jackson.
The alpha, Derek’s uncle, Peter Hale, tries to convince Scott to join his pack by giving him memories of the fire. He hopes that Scott will by sympathetic to his cause once he sees how much he suffered. Scott refuses. Scott then interrupts Chris Argent's ambush of Jackson and tells Jackson he doesn’t understand the implications of what he’s asking. Scott claims he can't protect Jackson, too, because he's already having enough trouble trying to protect his real friends. Allison comes to Scott's house to try to make up, but they’re interrupted by Peter Hale arriving to take Scott’s mom on a date.
Scott wakes up in his boss's clinic, completely healed of his wolfsbane infection. Alan steadies him. Scott picks up Peter's presence. Alan is however unafraid of the murderous Alpha. Peter is somehow unable to enter. Peter says there are others who are more defenseless to get Scott to join him. Scott figures out he means Allison. Scott leaves having no chance to ask his boss how he's connected to werewolves.
He comes home and alerts Stiles, but can't seem to find his phone. Scott starts watching over Allison around the clock. Scott learns from Coach he's banned from the winter formal due to his failing grades. He asks Jackson to go with Allison to keep her safe. He wolfs out in Jackson's face when the latter refuses out for his own safety. Jackson agrees, but Scott decides to go anyway. While his mom fixes up his suit, he tells her that he really loves Allison, and she advises him to tell her "anything and everything" he wants. She doesn't know it, but Scott takes her advice to mean that he should tell her about being a werewolf.
Allison takes Scott out to make out in a bus. Allison goes inside luring him in. Suddenly Chris Argent and another hunter show up in their cars. They charge at Scott with their cars, forcing him to jump up and transform. Scott looks up and he has shifted in front of Allison.
Scott releases one of Derek's shackles and attempts to blackmail him into helping in return for freeing him the rest of the way. Derek demands he get him out regardless. Scott shows Derek the picture of the deer with the spiral carved onto it. He tells Derek his boss told him a person, Nurse Jennifer came into the clinic asking for a copy. The picture is what lead Laura back to town: Peter and Jennifer lead her back so Peter could kill her and become an Alpha, so Peter lied when he said he'd killed Laura accidentally. Derek frees himself from the remaining shackel and tells Scott he'll help him.
Scott and Derek head out together. Kate and a resolved Allison attack them. Scott attempts to tell Allison he was going to tell her everything at the formal, and all his lies were to protect her. Allison coldly tells him she doesn't believe him. Kate moves in to shoot Scott, to which Allison protests but Chris Argent stops Kate after learning she was the one who set the Hale Fire, breaking the hunter's code from Stiles. Chris holds Kate at gunpoint to have her take her gun off Scott.
Over the next few weeks, in the aftermath of Peter's defeat, Scott and Stiles keep watch over Lydia as she recovers. They are surprised she's alive but not becoming a werewolf. Scott reconciles with Allison. With Scott exposed as a werewolf, Chris and Victoria vehemently forbid he and Allison from seeing each other ever again. To this end, when Chris catches them during one of their rendezvouses he brutally holds his gun to Scott's face forcefully having Allison promise she'll stop seeing Scott to prove his point.
Scott and Allison don't listen however, and recklessly carry on their romance in secret maintaining a facade at school with secret messages and clandestine meeting places, eventually consummating their relationship.+.