They stop when Scott hears the controls on her dad's SUV. Scott hurries outside the window with his discarded clothes before Victoria Argent enters Allison's room. After Victoria leaves, Scott hears a distant scream. He recognizes it as Lydia's.
Scott heads to the hospital where Lydia has disappeared to find Stiles already there. Stiles hands him Lydia's hospital gown to use his sense of smell to track her. They are about to take off when Allison appears in front of them. Scott worries that someone could see her with them. Allison tells him Lydia is her best friend and they have to find her as she just saw her dad and three other men leave in SUVs, "a hunting party". She gets in and they leave with Scott following the scent.
At school the following day, Lydia has still not been found, as Scott hears from Stiles that she was at Beacon Hills Cemetery. Scott leaves a discreet note at Allison's locker. He grins when she reads the note "Because I love You." Scott senses Allison's distress from the other students' gossip over Kate being convicted for the murders. He pulls her into the chemistry classroom and comforts her. He tells Allison there's "No Peter," and that he'll be at the funeral, just not in plain sight.
Scott discreetly looks upon the funeral which is in chaos because of the media. Stiles later joins him. Scott catches Allison's eye and waves at her. Scott sees Allison being greeted by Gerard Argent. They are caught however by a pissed off Sheriff Stilinski. Over the police's frequency, they hear of an ambulance being attacked. They escape Stilinski. Upon seeing the ambulance's victim in bloody shreds, Stiles implores him to "find her". Scott hurries off into the woods. He eventually catches the sight of a animalistic shape fleeing and gives chase. He catches up to the fleeing werewolf, but sees it's not Lydia, but an unfamiliar man.
Derek forces Scott to watch as Gerard kills the werewolf by bisecting him with a broadsword, telling him this is what hunters do and why they need each other. Scott, horrified asks what is happening. Derek replies "Declaring war."
Scott smells another werewolf in the locker room. On the field, he realizes it's Isaac. He and Stiles try to figure out how to free Isaac from jail and keep Scott from hurting anyone during the full moon. Derek takes him to Issac's house to show him that the young man was being abused by his father and says that is why he chose to become a werewolf. Allison is confronted by a lizard creature and Scott wolfs out and scares it away.
Scott catches Erica who falls from a climbing wall during a seizure. He and Stiles go on a double date with Allison and Lydia to the skating rink. After Erica becomes a werewolf, Scott and Stiles try to figure out who Derek will target next. Once he figures out that Boyd will become the third pack member, Scott sets off to talk him out of it but ends up in a battle with Isaac, Erica, and Derek.
Scott learns about a book the hunters have that will detail all the creatures they've seen. At school, Scott and Allison continue to pretend to be broken up as Stiles runs messages back and forth between them plotting how to find the bestiary. During the lacrosse game, Scott breaks his leg but it heals almost instantly. Gerard invites him to dinner, where Scott breaks into Gerard's safe looking for the bestiary but finds only a cookbook. Scott then rushes back to the school and saves Stiles and Derek from the kanima. Later Gerard stabs Scott in the gut and threatens his mother.
Scott tries to keep Lydia safe after Derek assumes she is the kanima. Matt begins to suspect something is weird about Scott because his eyes cause a lens flare in all photographs. Scott realizes Derek doesn't know as much as he might think and tries to convince him that Lydia might be immune to the bite. Scott, Allison, and Stiles beat Erica and Isaac in a fight at Scott's house leading Derek to believe that Scott is already an alpha of a his own pack made up of his human friends. This is a symbolic statement as Scott clearly still has the eyes of beta.
Scott chases Jackson to a dance club called Jungle. He gets hit on by a guy and then tries to protect Danny from the kanima. He finds Jackson in human form in the parking lot and with Stiles' help locks him in a police van. He then tries to figure out why Jackson would be after Danny and learns of the full moon video. his mom says he's failing two classes and he promises to do better. Scott and Allison make out and Jackson escapes.
Jackson secures a restraining order against Scott and Stiles. Scott's mom grounds him and takes away his car keys and Stiles privileges. Scott allows his mom to think that he's having issues with his dad being gone rather than tell her the real things that he's struggling with. Allison delivers information about the kanima to Scott and Stiles in the library so they don't get caught on camera. Allison thinks that Jackson is a kanima instead of a werewolf because of his birth parents and offers to ask him about it. Scott doesn't like it but can't stop her. While taking his makeup chemistry test, Scott hears Allison's heartbeat increase. He tracks her to the locker room and finds a naked Jackson on top of her on the floor. Scott starts throwing Jackson around the room and Jackson responds in kind. They wreck the boys locker room. They fight until Mr. Harris shows up and gives everybody detention. At detention Jackson, under the control of the master, threatens to kill them all, Scott reluctantly joins Derek's Pack, but only on the condition that they save Jackson rather than kill him.
Scott tracks Jackson to an abandoned warehouse where he's buying a ticket for a rave. The host is the kanima's next target. Scott, Derek, and Isaac meet with Dr. Deaton to discuss how they can stop the kanima. Deaton thinks that if they can affect the kanima, they can affect the master, and he suggests using mountain ash to contain them at the rave. When the time comes to implement the plan, Scott learns that Allison's father is at the rave hoping to kill Jackson. He gets angry at her for interfering with their plan and walks away to deal with the problem leaving Allison upset. Scott gives Isaac the ketamine needle to subdue Jackson because he has to go take care of the hunters. On his way out, Scott is hit by an SUV driven by Allison's mom. She puts him in a room with a cannabis vaporizer filled with wolfsbane. She says his death will look like an asthma attack. Scott is overwhelmed by the vapor and close to death, but manages to howl and Derek comes to his rescue. Derek brings Scott to the Animal Clinic to recover and later that night they regroup at the subway tunnel hideout. Scott realizes that saving Jackson probably isn't possible, but Derek doesn't know how to kill it either. Scott thinks Derek is hiding something, but Derek just tells him to go home.
Scott attends Lydia's birthday party. He's under the influence of the full moon and not particularly friendly toward Lydia when they realize that no one has come to her party. At Allison's prompting, Scott calls the lacrosse team and gets them to show up. There's distance between Scott and Allison since he yelled at her at the rave. Stiles suggests that Scott apologize, but Scott won't because he doesn't think he did anything wrong. He admits that the full moon is probably clouding his judgment. When Lydia finally convinces him that he should try to have a good time, he drinks some of her punch spiked with wolfsbane. This causes him to hallucinate Allison making out with Jackson and then the kanima. Scott finds Stiles passed out drunk and wakes him up because he needs his help in figuring out what's going on. They see Matt get thrown in the pool, screaming that he can't swim, and then Jackson saves him. Scott doesn't notice Allison leave the party for the hospital. After the party is broken up by the cops, he sees Matt and the kanima together and realizes Matt is the kanima's master.
Scott and Stiles go straight to Sheriff Stilinski with the news about Matt and try to convince him to investigate. They get him to go to the sheriff's station to look at the evidence and Scott spots Matt on the hospital security cameras. They see Matt talking to Scott's mom, and Scott calls her to see if she remembers him. She does and agrees to come down to the station. Matt shows up at the police station and holds Scott, Stiles, the Sheriff, and Mrs. McCall hostage along with Derek, who was paralyzed while coming to help Scott. Scott gets shot and eventually has to reveal to his mother that he's a werewolf. She gets upset and doesn't want to talk to him about it. The Argents show up looking for Derek and Scott sees Allison but doesn't know why she's suddenly so cold and on the hunt. Scott runs into Gerard in the station and complains that this wasn't the plan they'd agreed on. Gerard drops his pill box and Scott returns it to him. Derek overhears their conversation, although Scott doesn't realize it.
Later Scott finds Gerard and the kanima in his room, threatening his mom. Gerard wants Scott to turn over Derek. Mrs. McCall tells Scott to do whatever Gerard asks. Issac comes to the animal clinic to seek advice after his pack mates decide to leave Derek. Scott wonders why Isaac would come to him for advice since they didn't trust each other a few episodes ago. Isaac tells him that he's always trying to do the right thing. Scott says that he can't leave. Issac decides to go with Boyd and Erica, but before he leaves he tells Scott that Jackson will be playing in the championship lacrosse game. Scott is forbidden from playing lacrosse due to his grades. Gerard threatens to start hurting people if Scott doesn't hand over Derek before the end of the game. Issac returns during the game and takes out several players so the coach will have to play Scott and he can keep a close eye on Jackson. Gerard has Jackson take out Isaac with some toxin, forcing Scott to leave the game so Isaac doesn't get cut in half. The team manages to win without them, but Gerard has Jackson attack himself on the field. He appears to be dead and Stiles goes missing.
After the game Scott and Isaac are going to track Stiles by scent, but Derek and Peter show up with a plan on how to save Jackson and stop Gerard. They all go to the Hale House, so Peter can get a laptop with the family's files on it. Stiles returns home in the meantime, which only Scott seems to care about. Scott gets a call from his mom telling him he needs to come see what's happening to Jackson right away. Isaac and Scott go to the hospital while Derek and Peter do research. While they are moving Jackson, Chris Argent shows up claiming he wants to help. With his help, Scott takes Jackson's body to a warehouse where Gerard and Allison are waiting for them. Gerard reveals his master plan to use Derek to cure his cancer with the bite. Scott grabs the paralyzed Derek and forces his mouth open despite his pleading so that Gerard can impale himself on his teeth. The bite backfires and Gerard realizes that Scott switched his cancer medication with pills of mountain ash. Gerard orders the kanima to kill everyone, but Stiles and Lydia show up,and Lydia is able to bring Jackson back to himself. Peter and Derek stab Jackson to finish triggering his transformation into a werewolf. Scott and Allison hold hands as they look on. Later, Allison breaks up with Scott, but he refuses to believe that it will be a permanent breakup.
Scott resolves to do better in the next school year. He and Stiles go to the field to practice lacrosse, and even though Scott promises that he won't use his powers, he can't resist doing so.