Isaac Lahey and his father are having dinner and discussing Isaac’s grades. There is very obvious tension between them, and Isaac seems to be incredibly fearful. After working very hard to work around the topic Isaac admits that he has a D in chemistry, and Mr. Lahey states that he has to “punish him” by having him clean the kitchen before beginning to push dishes off the table, causing them to shatter on the floor. Isaac immediately jumps up from the table and goes to duck and cover in the corner, suggesting that this has happened before. Mr. Lahey throws a glass at him that this the wall just above his head and shatters, causing a shard of glass to get stuck in his skin just under his eye. When he pulls it out it heals almost immediately, and Isaac runs out of the house, taking his bike. Mr. Lahey follows him in his car, and Jackson, who lives down the street, comments that they (the Lahey’s) are freaks. It begins to pour outside. Mr. Lahey sees Isaac’s bike in an alley and gets out of the car, calling his name. He sees a blurry figure without his glasses on, but then it’s gone. A reptilian monster rips off the car door before killing him.
Allison is seen sneaking out of her house, finding a message on her car’s window that reads “midnight”. She heads out to the cliff overlooking the town in the preserve where she meets up with Scott who starts asking about Gerard. Scott tells her that they have to be more careful, and they kiss. Chris Argent approaches the principal of Beacon Hills High School with a gun, with two bulky men behind him. Victoria Argent brings the principal into the car and electrocutes him with one of their tasers. Isaac runs into the subway station to find Derek. He tells Derek that his dad is dead, but it wasn’t his fault.
At the school the next day, Scott and Stiles are talking about the upcoming full moon. Stiles believes that Scott should still be locked up as a precaution, and he opens his locker where a long length of chain falls out. Coach Bobby Finstock makes a sarcastic comment and Scott senses another Werewolf in the locker room. Allison and Lydia walk up to the school with Allison giving Lydia a pep talk about being back at school after the incident in the woods. When Lydia walks in everyone stares as predicted, and she pretends to be unaffected.
At lacrosse practice, Scott plays goalie in hopes of getting the players one on one. He decides to tackle them all and then sniff them in hopes of finding the Werewolf. This happens four times before Jackson decides that he’s hurt so he won’t participate, and Scott realizes the new werewolf is Isaac. Sheriff Stilinski and his team show up to investigate the murder. Stiles tells Scott that Isaac will most likely end up in a holding cell for twenty-four hours, meaning he’d be at the police station for the night of the full moon, and Scott replies that he will probably "have the urge to maim and kill."
During a chemistry class Danny Mahealani reveals that the police are talking to Jackson, thinking that he may be the witness they needs to hold him since he’s underage. Scott and Stiles purposely get themselves sent to the principal’s office to intervene. Jackson knew about the abuse and insists that it wasn’t his problem. Sheriff Stilinski gives him a disgusted look before saying “…it’s funny that the kids getting beaten up are always the ones that least deserve it.” Jackson doesn’t get it. Stiles epically fails at hiding behind a magazine when his father comes out of the office, and his dad ignores him, but says hello to Scott. Gerard is revealed as the new principal of the school.
In the principal’s office, Gerard looks over Scott and Stiles’s student records and adds commentary before saying that one of them will have to stay for detention. It’s implied that Stiles gets it. Lydia tries to talk to Jackson at his locker, but he obviously isn't very interested in her right now. Jackson rejects her even though she didn't really ask for anything—only thanked him for saving her—before telling her that she shouldn't go to the game that night because of the full moon. Scott sprints out of the school to see the police driving away with Isaac. Next Derek pulls up in the Camaro, telling Scott to get in. Scott is mad that Derek's turning people, but Derek eventually gets him in the car by telling him that there is evidence in the house that is much worse than anything Jackson could have said.
That night, Gerard and Chris Argent are in the study at their house. Gerard wants to “eliminate the threat” if there’s proof that Isaac’s a Werewolf, but Chris isn’t totally on board with that plan. He says that the ripped off door of the Lahey car is potential proof that Isaac is a werewolf, although it’s not irrefutable. Gerard catches Allison watching and Chris closes the door to the study.
Matt Daehler brings the video camera to Jackson’s house and Jackson pays him. Matt thinks Jackson is planning to record a sex tape with Allison since he asked for something that’s good and low light and could stay recording all night long, but he insists that he’s just “documenting history”.
Scott and Derek have arrived at the Lahey house. Derek calls Scott out on the way he was tackling and sniffing his teammates earlier to try and find the werewolf. He’s not impressed. Allison notices a weird police officer in their house before her dad and grandfather call her into the study. Derek sends Scott into the Lahey's basement, wanting him to use his senses to find the evidence he mentioned earlier: a motive. Derek is cryptic as usual, but eventually Scott finds a commercial sized freezer with bloodied scratch marks on the lid, suggesting that Isaac was locked in it. As Stiles gets out of detention he gets on the phone with Allison. They are discussing a plan to stop the hunter that the Argents just sent to the police station to kill Isaac.
Scott is once again yelling at Derek for turning people, and Derek insists that he has every right as long as there is informed consent. Scott can’t comprehend how someone would still want the bite after knowing everything that comes with it, but Derek fires back that he’s the idiot dating a hunter’s daughter. Scott is shaken when he realizes that they are so obvious that Derek, who doesn’t spend a whole bunch of time with them, still knows, and Derek turns the conversation into a sales pitch for joining the Hale pack. Scott refuses because he’d lose Allison, but he agrees to cooperate with Derek anyway.
Jackson sets up the video camera in his bedroom to record him while he’s sleeping. The hunter disguised as a police officer is on his way to the station when Allison shoots three arrows into his tire, and then another into his leg when he gets out of the car to check it. Apparently this was part of a plan to slow him down. Stiles is on his way to the police station. Allison arrives to the Lahey house where Scott is in the basement, trying to keep from shifting. They have agreed to lock him in the freezer, secured with Stiles’s chains. Isaac begins to shift in his cell at the police station. Allison helps Scott into the freezer and secures the chains.
Stiles shows up at the police station with Derek. They are making a plan to get Isaac out. Derek has no plan as usual, and Stiles forces him to think about it before sprinting into action. Derek flirts with the lady at the front desk so Stiles can sneak past. Allison finishes the chains on the freezer and heads upstairs to leave the house. Stiles goes to get the keys to the cells from his father’s office, but they’re already gone. The hunter has taken them and he’s limping toward the cells. Allison is on her way out of the Lahey house when her flashlight dies. She hears loud breathing other than her own and then sees something and screams. Scott hears it and starts trying to break out of the freezer. The hunter covers Stiles's mouth and drags Stiles into the holding area, but Stiles manages to hit the alarm on the way. Isaac’s cell has been busted open and he appears from behind them, attacking the hunter. Isaac knocks him out just before Derek arrives. Derek destroys the wolfsbane before half shifting and roaring at Isaac who immediately drops to the floor and cowers, shifting back to his human form. Stiles asks Derek how he did that and he replies haughtily, "I'm the Alpha."
Scott continues to fight the freezer until the chains and lock finally snap and he runs upstairs, fully shifted. There is a reptilian-humanoid creature crawling on the ceiling. It runs away without attacking. Sheriff Stilinski and other deputies walk into the holding cell area. Isaac and Derek are both gone, the hunter/deputy is knocked out on the floor and Stiles is just standing there, seemingly unaware of how bad this looks. Jackson wakes up suddenly the next morning and goes straight to the camera. He doesn't find what he's looking for, and he throws it to the ground. The episode ends with him trying to convince himself that nothing happened.