Isaac works for his father at the Beacon Hills Cemetery. He's working late one night digging a grave near Kate Argent's grave when he sees something among the headstones. He stops the backhoe to take a closer look, but suddenly the backhoe gets overturned, and Isaac is dumped into the grave he was digging, with the machinery on top. Just as suddenly, the backhoe lifts, and Derek Hale asks Isaac if he'd like some help.
The next morning, Sheriff Stilinski interviews Isaac and Mr. Lahey about the desecration of Kate's grave. Isaac's dad is threatening, and the Sheriff picks up on the hostility and Isaac's black eye, but he can't do anything unless Isaac makes an accusation. Over the Sheriff's shoulder, Isaac sees Derek at the tree line. He reports to the Sheriff that the graverobber took Kate's liver.
That evening, Isaac finds Derek in the subway tunnel hideout and accepts the Bite. As someone who is abused, it is presumably the offer of power and control that convinces him into the choice.
The next day during dinner, Isaac tells his father about his poor grades, and his father starts to yell. He throws a glass at him, which shatters, and a shard sticks into Isaac's cheek just under his eye. When he pulls it out, it heals, and his father is stunned. Isaac runs away and takes his bike. Jackson sees them arguing and scoffs. Mr. Lahey gets in the car and goes looking for Isaac. Eventually, he sees Isaac's bike abandoned in an alleyway, but when he stops to investigate, he is attacked and killed by the kanima. When Isaac realizes that his father is dead, he goes to find Derek and tells him that he didn't kill him.
A few days later, the police take Isaac away for questioning in his father's murder. The problem is that they've done so on the night of the full moon. Derek and Scott both know that Isaac can't be in police custody when the full moon rises, because he won't be able to control his bloodlust. Stiles and Allison discover that the hunters plan to kill Isaac while he's at the station, and they hatch a plan with Derek to break Isaac out. They arrive a little too late. Isaac has already shifted and busted out of the holding cell by the time Stiles and Derek arrive. Isaac takes out the hunter on his own and his about to attack Stiles when Derek gets between and growls Isaac into submission. They leave the station, and Isaac is now a fugitive.
Derek turns Erica and then Boyd. They go to confront Scott at the skating rink; Scott doesn't know that Boyd has taken the Bite and wants to convince him out of it. Isaac tells Scott that aside from being a fugitive, life is pretty good. Erica is even happier with her new Werewolf powers They both attack Scott at Derek's behest, but Scott defeats them both. He can't defeat Derek, though, and is left with some slow-healing wounds.
Because of their poor performance at the skating rink, Derek starts Isaac and Erica on combat training. Isaac takes the exact same route a number of times and gets thrown down by Derek each time. Derek gets annoyed at their predictability. Isaac asks if they can take a break so his bones can heal. Derek comes over like he's going to be comforting and then breaks Isaac's arm as punishment for complaining. He's trying to teach them to survive, and there's no room for resting.
Isaac stays hidden in the subway tunnel hideout while Derek and Erica try to investigate the reptile creature more. Once Derek realizes it's a kanima, he has Erica bring Jackson to the sunway tunnel hideout to test him. He has a piece of mirror with kanima venom on it and figures that whoever the kanima is will be immune to the venom. Isaac helps hold Jackson down while they administer the toxin. When Jackson fails the test, they tell him that he's going to do a favor for Isaac anyway.
They make Jackson recant his story about seeing Isaac and Mr. Lahey fight on the night of the murder. Without that testimony, Isaac is no longer a suspect. The freezer that he was locked in has since been destroyed, so there's no physical evidence of his abuse left. With the charges dropped, Isaac is able to come back to school, much to the chagrin of Scott and Stiles. Since Jackson passed the kanima test, Derek has Isaac and Erica test Lydia.
In Chemistry class, they are going to do a group experiment and rotate partners. Isaac ends up with Stiles. Stiles threatens to hurt him if he hurts Lydia. Isaac replies that he asked her out once and she pretended that he didn't exist. Now he's going to turn that hurt into killing her. They rotate partners again, and Isaac sits with Lydia. They complete their experiment properly, creating a sugar crystal, and Isaac puts kanima venom on it before offering it to Lydia to eat. She does, with no ill effect, and therefore fails the test.
Everyone assumes that Derek is going to be the one to kill Lydia, but he's actually assigned this job to Isaac and Erica. They go looking for her in the library. As they flounce down the hallway in their leather with their attitudes, Isaac scrapes his claws along the lockers, throwing up sparks. Isaac grabs Matt in the library and demands to know where Lydia is, but he doesn't know what he's talking about. Erica and Isaac then regroup with Derek and follow Stiles, Allison, Jackson, and Lydia to Scott's house.
Isaac ends up going in first. He goes in the back of the house and is able to sneak up on Allison and Stiles. He attacks them both, and then Erica comes in to join the fight. At some point, Scott arrives and takes out Isaac, while Allison has already dealt with Erica. Scott tosses both betas out of his house onto the ground in front of Derek. Since the police are already on their way, they have no choice but to leave. Everyone sees the kanima crawl along the roof of Scott's house and escape. Boyd takes Erica and Isaac back to the subway hideout while Derek chases down and confronts the kanima.
A few days later, Derek explains to Erica and Isaac that they need to get closer to Scott and Stiles because they might know something useful about the kanima. Isaac thinks that maybe they should leave the kanima business to the Argents. After all, the Argents are trying to hunt them down, which is a pretty big threat all on its own. Derek tells him that they can't forget about the kanima because Gerard was acting really strange around it. He wasn't afraid of it, and that has Derek worried. Isaac also expresses worry about Derek chaining them up for the full moon, because it will leave Derek defenseless.
Erica is able to confirm that Jackson is the kanima, and Isaac joins in on the plan to capture him. Scott, Isaac, and Derek go to Dr. Deaton to seek his advice on how they can deal with the kanima. Scott isn't happy to see Isaac and claims he doesn't trust him. Isaac replies that he doesn't trust Scott either. In the exam room, Isaac goes to touch some of the bottles that Deaton has, but Derek grabs his wrist to stop him, admonishing him not to touch things when he doesn't know what they are. Deaton tells them that he doesn't have anything that can protect them against the toxin, so Isaac asks if he has any offensive suggestions. They figure out that the kanima shares the fears of the master, so Deaton reasons that if something affects one it affects the other. He suggests capturing the kanima with mountain ash, which should also capture the master.
They know that Jackson is going to be at the rave on Friday night, but Scott and Stiles can't figure out how to get tickets. Stiles tries begging them from Danny in the locker room, but Danny won't give them up. Isaac gets frustrated with their ineptitude and watches another guy in the locker room get handed two tickets. He then goes over and beats the kid up to take them.
That night, Isaac and Erica head into the rave to find Jackson. They are to provide distraction while Scott administers a shot of ketamine. The plan starts going awry when Scott learns that the Argents are also at the rave. He gives Isaac the ketamine needle and tells him to be careful because he doesn't want him to get hurt. This is the first time that Scott has expressed any care for Isaac's well-being, and Isaac's long stare communicates both his disbelief and thanks at the gesture. It was only a day or so prior when both he and Scott expressed their mutual distrust.
Isaac and Erica find Jackson and start dancing with him. The boys both kiss on Erica and give each other intense, lustful looks. Just when Isaac is about to give Jackson the shot, Jackson claws them both in the gut. Isaac is able to recover enough to go through with the injection, and he pulls Jackson out of the crowd. They set him up in a side room and wait for Stiles to arrive. Once Stiles is there, Isaac attempts to find out just how out of it Jackson is by attacking him. Jackson grabs and breaks Isaac's wrist without seeming to be conscious. Stiles takes over interrogating Jackson and the master while Erica and Isaac watch. When Jackson starts to fully transform, they run out of the room and slam the door shut, but the kanima breaks through the wall instead.
They all run to find Derek, but Isaac and Erica can't cross the mountain ash line that Stiles had laid around the rave. Derek quickly makes him break the line so he can save Scott. Presumably Isaac and Erica return to the subway tunnel hideout while Derek takes Scott to the Animal Clinic.
The night of the Worm Moon, Derek opens a trunk and starts taking out chains and other restraints. Isaac asks about the symbol on the box, the same as his tattoo, and Boyd responds that it's a triskele. It can mean many things, and Boyd guesses that for Derek it means alpha, beta, omega. Derek explains that it means that any werewolf can rise or fall to any status. Isaac asks about Scott being an omega, but Derek corrects him and says that he's a beta because he's part of the pack. Isaac wants to know how Scott can be part of the pack if he isn't there with them. Derek tells him that he's out looking for Jackson.
When Derek starts chaining them up in the subway car, Isaac asks why Erica has to wear the headband. Derek tells him that she can withstand more pain than the boys and then offers Isaac a headband if he really wants one. He declines and helps hold Erica down while Derek tightens the screws on the headband into her skull. Isaac is the last to be chained. Derek locks him onto a seat in the subway car. Isaac asks him how he doesn't feel the bloodlust. Derek replies that he does but he has an anchor that keeps him in control. His anchor is anger, but it doesn't have to be that for everyone. Isaac realizes that he means Scott. Once Derek is done with the locks, Isaac tries pulling on them and pulls up the seat that was bolted to the floor. Derek doesn't have any time to fix it, though, because Erica and Boyd start changing and breaking out. While Derek deals with Erica, Isaac breaks free and leaps out the car window. He returns to help Derek and holds Boyd down while Derek chains Erica back up. They look at one another and nod.
Derek tells Isaac that he think he's going to be able to control himself on the full moon now. He asks what anchor Isaac found, and Isaac replies that it's his father. Even Derek thinks this is weird since his father locked him into a freezer to punish him. Isaac replies that he didn't always do that.
While Derek is gone dealing with Matt and the kanima, Boyd and Erica decide that they want to leave. Being hunted by the Argents is too dangerous. They ask Isaac if he wants to leave as well. No one has seen any of them for some time, so they are considered runaways. Erica and Boyd are sure they want to go, but Isaac goes to Scott for advice. He goes to see Scott at work at the Animal Clinic. Isaac asks why the dog that Deaton and Scott are treating smells bad, and they tell him that it's because the dog has cancer. Isaac seems particularly affected by this and on the edge of tears. Deaton then shows him that he has werewolf powers that can be of benefit to others and has him touch the dog. Without even trying, he starts to siphon pain out of it. Isaac cries, and Scott tells him that he cried the first time too. Scott says that he's staying because he has a life here and people he cares about. Isaac replies that he doesn't have anyone. That makes him decide to go. He wishes Scott well in the lacrosse championship, but Scott says that he isn't playing. Isaac tells him that Jackson is back and playing on the team and will be in the championship, which gives Scott a reason to play.
Scott is benched at the game because of his grades, but Jackson is on the field. Isaac doesn't leave with Boyd and Erica as he said he was going to and ends up coming to help. They need to get Scott on the field, but there are a bunch of players already in reserve before Coach Finstock would have to play Scott. Isaac offers to injure players on their team until Scott has to get into the game. Scott asks him not to seriously injure anyone, and Isaac only offers to try. He manages to take out the other players but himself becomes the final injured player that forces Scott into the game. Gerard had Jackson poison Isaac with toxin, paralyzing him. He's taken off the field, and then Gerard and two hunters come after him in the locker room. Gerard has a sword and is planning to cut him in half. Isaac crawls away and pulls himself up on a sink to face Gerard. This lets him see Scott come up behind the hunters and attack.
The Cyclones win the game, but Jackson stabs himself in the stomach with his own claws and Stiles goes missing. The Sheriff talks to Isaac and Scott in the locker room, asking them to call if they hear anything from Stiles. Isaac promises that they will. After everyone is gone, Scott rips open Stiles's locker and gets out some of his clothes. He gives Isaac a shoe, and Isaac asks why he gets a shoe with Scott gets a shirt. They plan to try to find Stiles by scent, but they don't get the chance because Derek shows up with the newly resurrected Peter. Scott didn't know that Peter was alive again, and Isaac has no idea who this guy is. He asks, and Scott tells him Peter tried to kill them all so they set him on fire and Derek slashed his throat. Peter has a plan on how to save Jackson, and Isaac replies that that's great except Jackson is dead. He wonders why no one thinks that's good news. Peter explains that Jackson is only dead if Gerard wants him to be, and they need to know why.
Scott's mom calls and reports that something weird is happening with Jackson. Isaac goes with Scott to check it out, and they find that Jackson is transforming and starting to move. Scott calls Derek, and they agree to take Jackson to the warehouse district. Isaac helps Scott carry Jackson outside, where they run into Chris Argent. Scott thinks Chris is there to get in their way, but Chris ends up offering to help.
They all end up in the warehouse with Gerard and Allison. Allison shoots Isaac with an arrow and Scott drags him to safety. Everyone begins fighting, with Derek mostly trying to take on the kanima on his own. When he gets swiped across the middle and paralyzed, Isaac tries to come to his aid, but Allison rushes up behind him to stab him with her ring daggers. Scott stops Allison from going after Derek, and they all watch as Gerard reveals his plan. They all watch as Gerard starts spewing black ooze, and then as Lydia helps save Jackson.