Scott starts Season 3 in a tattoo parlor. Scott wants a tattoo of two bands around his arm, but his werewolf healing makes it disappear soon after. He and Stiles spot Lydia and Allison on the road at night and try to talk to them, although the girls don't want to. They end up stopping in the middle of the street, and Lydia's car gets hit by a deer.
Scott tells Stiles that he wants to ask Derek about tattooing since he obviously got the triskele to stick. Stiles comments that Derek probably has bigger things to worry about, gesturing at missing persons posters of Boyd and Erica.
He's awkward around Allison during class, but before they can talk about it Scott gets called to the hospital by his mom. Melissa tells Scott where Isaac is. A blind man enters the elevator with Scott. Scott spots Isaac’s nurse taking him into an elevator. Scott attacks the nurse, an alpha, and is saved by Derek.
Derek and Scott bring Isaac to the Hale House so Derek can get something to help Isaac. Scott tells Stiles to meet him there. Scott tells Derek that he could repay the favor Derek owes him for having showed up to try to help Isaac by making his tattoo show, which involves a blowtorch. On his way out, Scott asks about the door being painted red. Scott claws at the door revealing the alpha pack symbol. Derek tells Scott that he, along with Isaac and Peter, have spent the last four months trying to get Erica and Boyd from the alpha pack.
The following day, Stiles and Scott are walking up to a house party that will be attended by kids from a different high school. Allison and Lydia arrive at the party and meet Scott outside to show him the marks that Braeden left on their arms.
Scott brings Lydia and Allison together with Derek at the school, but Derek doesn’t recognize their marks as any type of symbol. Derek is not impressed that this is Scott’s attempt to help because neither girl have been good for him. Derek’s thinks that maybe Scott should actually tell Allison what the situation was when Derek bit her mother.
At school, twin werewolves show up. In order to find Boyd and Erica, they decide to put Isaac in ice water until his heartbeat slows enough for Deaton to have access to his subconscious and find his memories. Between Scott, Stiles, and Derek they manage to keep him down. He reveals that they're being held at Beacon Hills First National and the other betas are locked in the vault.
Scott and Stiles spend the night researching the bank but they don't have anything useful. Scott insists on being optimistic about it, and right after his pep talk Stiles discovers that his dad worked on the case. At his apartment, Stiles explains how the robbers managed to get in. Derek decides that he can punch through the wall, and uses Stiles’s outstretched hand for a demo, to Peter’s amusement and Scott’s annoyance. Derek asks Scott for his help, and Scott agrees that he’ll try, although he’s focused on who the other girl with Boyd is.
Derek and Scott reach the vault, and Scott’s worried that there’s a bunch of risk that they can’t evaluate. Derek punches out the wall as promised, and he and Scott enter the vault. Ms. Morrell closes the mountain ash circle around the vault and the wolves shift, finally able to feel the moon.
Allison watches the fight, shocked, before breaking the mountain ash seal on the vault against Derek’s warning, and both Boyd and Cora run out. Derek is furious, explaining that now the two of them are going to go kill anything they can find. Derek again mentions her mother, and Allison realizes there's something she needs to know.
Scott and Derek take off after Boyd and Cora. Scott finds two kids who Boyd almost killed and has to escort them home. They next find Cora attacking a girl in the woods whose girlfriend has disappeared. Scott advises the girl to get out of Beacon Hills Preserve.
Stiles then calls to tell them that someone has been murdered on the other side of town. Derek doesn't think it could have been Boyd and Cora, but Scott disagrees. He thinks they're in over their heads and wants to ask Chris Argent for help. Chris is retired because the supernatural destroyed his family. Scott tells him that they need him because it will save innocents. Chris refuses to help but does agree to give Scott a ride to the pool. Scott knows that Chris will see the victim first-hand, and as he predicted, Chris agrees to help and tells them that they’re footprint tracking is flawed.
Neither Scott nor Derek are confident that they can track either of them by scent, although that would probably be the most effective method. Chris suggests trapping them in the school if there’s a location secure enough, and Isaac suggests the boiler room. They plant emitters leading toward the school. At the school, Scott and Isaac put in place the final preparations to trap Boyd and Cora.
Allison has decided to help on her own and brought flashbomb arrows to get Boyd and Cora into the building. Derek and Scott use themselves as bait to get Cora and Boyd into the boiler room. They spray fire extinguishers, hoping to confuse them before sprinting out of the boiler room and locking the door. Both Scott and Derek seem shocked that their plan actually worked, until Scott notices another heartbeat in the room.
Derek decides to go in against Scott's advice. Scott and Isaac go in after the sun has come up. Scott then goes to the hospital to meet with Stiles, who wants to show him the bodies that he no longer thinks are werewolf kills. Stiles explains that all the dead were virgins killed ritualistically.
Scott helps Deaton at the clinic. The dog’s owner tries to get the dog in the car, but he’s skittish and runs off. In the stool sample Scott finds mistletoe, poisonous to both dogs and werewolves. Scott hears sounds outside and goes out to find the dog's owner missing. At school the next day, Scott tells Stiles about the guy at the vet in the locker room before cross country practice and Stiles tries to find out if he’s virgin, because he still thinks the sacrifices are all virgins.
The Alpha twins approach Isaac during practice and Scott tries to reason with him, but Isaac refuses to listen. Isaac seems to lose them on the trail before he’s suddenly attacked and shoved down a shallow hill. Scott intervenes before they can actually hurt him, and all four wolves have partially shifted before they hear a scream and find the guy from the vet, killed like the others.
In Mr. Harris’s physics class, Scott tries to convince Isaac to leave the twins alone. Isaac excuses himself to the bathroom, and Scott tries to follow, but Harris won’t let him and the twins end up framing Isaac for beating up Ethan. Scott tries to keep Isaac from getting upset before noticing one of the twins, Aiden trying to cosy up to Lydia. Scott’s inevitably pissed, and Isaac is slightly amused.
At detention, Isaac and Allison enter the closet and Isaac is immediately set on edge by the small space. The door shuts, and Isaac begins to panic. He eventually shifts and attacks Allison before Scott gets them out and gets Isaac under control. Scott, Allison, and Isaac decide to get back at the twins by hot-wiring Aiden's motorcycle and driving it into the school. Ms. Blake catches Aiden with his bike.
Isaac and Scott are walking through the hall after school when the twins appear. They strip off their shirts, leaving Scott and Isaac confused, before combining into the larger alpha. Isaac’s ready to fight, but Scott pulls him away. The fight never happens because Deucalion intervenes.
That night, Scott is working at his desk when he hears a knock and Isaac enters, soaking wet and asking for a favor. Derek has thrown him out of the loft to keep him safe, and he wants to stay with the McCalls.
The following week, the cross country team is on a bus going to a meet. Scott is looking worse for wear and a flashback is shown of him in wolf form. Stiles wants to talk about what happened, but Scott is trying to avoid it. Scott has two massive gashes on his torso that are taking longer to heal because their from an alpha. Scott says that he “can’t believe he’s dead,” he being Derek.
A flashback shows Scott confronting Allison about a titanium arrow that he found at the school. Allison insists that she can take care of herself. They begin to discuss if Allison could actually take a Werewolf in light of the new alphas in town. For a moment in seems like play-fighting is going to lead to kissing, but Allison backs off. Scott proves his point when he easily pins Allison against the wall, and Scott begins to feel guilty. Scott closes by saying that his goal was to warn her about the alphas, not dominate her.
Scott walks into the Hale loft to tell Derek that he knows where the alphas are after meeting Deucalion in the elevator at Allison’s building, but they already know and are forming a coup de main or preemptive strike.
In present time, Scott’s wound starts bleeding again, and Stiles points out that bleeding means that it’s not healing at all. Scott notices that Ethan is listening, but doesn’t think Ethan will try anything with that many people around. Stiles points out that Boyd and Isaac are just ticking time bombs, but Scott doesn’t think they’ll do anything either.
The flashback picks back up at planning the fight in the loft. Scott doesn’t like the plan to just go kill everyone, and Peter makes a smart comment while Cora asks why “this kid” is necessary at all. Derek points out that Scott helped to save Cora’s life. When Scott says that there’s no way to kill that many alphas, Cora corrects that they’re only trying to kill one, Deucalion.
A conversation between Scott and Deaton is shown, where Scott is afraid that Derek is going to get his entire pack killed and wonders if he should try to stop them. Deaton tells him that he shouldn’t stop them, but lead them. This leads Scott to set up a meeting with Deucalion in the abandoned mall. When he goes to the meeting to talk, he has to take Isaac with him. To his surprise, Derek's Pack shows up to the meeting along with the rest of the alpha pack. Fighting ensues.
Back on the bus, Scott tells Boyd that he needs to calm down because he can’t do anything to Ethan right now. When Boyd tries to fight, Isaac helps to keep Boyd in his seat. The movement causes Scott’s jacket to shift, and Isaac asks about the blood. Scott says he’s fine and asks Boyd to wait for him come up with a plan.
They eventually learn through Danny that Ethan is worried that someone he knows might not live through the night. This can only be Ennis, who fell with Derek. When Scott can't get through to Deaton, Stiles decides to call Lydia and Allison, who he knows have been following the bus. He tells them about Scott's wound, and they tell him he has to get the bus to pull over.
They manage it and get Scott into the bathroom and realize that he's not letting himself heal because he feels guilty about Derek being dead. Lydia suggests stitching him up to make him believe that he'll heal. Stiles and Lydia leave to get Scott’s bag and make sure the bus doesn’t leave as Allison prepares to stitch Scott up. Allison is beginning to get visibly upset and can’t thread the needle. Allison finally gets the needle threaded and begins to stitch Scott up. Scott has no reaction. Allison finishes the stitching, but Scott is still not responding. Apparently he’s stopped breathing.
Allison finally gets through to Scott, who says that it’s his fault, although the viewer has seen nothing to suggest that. Allison helps him stand and gets him a new shirt. They leave the bathroom to find Isaac beating up Ethan. Scott yells at Isaac to stop.
Now that he's healing, Scott thanks Allison for showing up on the night of the fight. Her intervention meant Derek didn't have to either kill Boyd or watch Cora die.
The cross country team's bus pulls up to the same motel, called the Motel Glen Capri. Apparently their meet has been postponed until the next day.
Stiles and Scott lie on their respective beds in their room discussing possible suspects for the sacrifices. Stiles mentions Derek, who was apparently on Stiles's original list twice, before adding Harris, their chemistry teacher. Scott is skeptical and asks if it's someone at school, considering that they had no clue about Matt Daehler being the kanima's master. Stiles sits up quickly to point out that he called that from the start, but no one took him seriously. Scott is mollified and asks who else is on Stiles's list.
Scott is disturbed when he sees his eyes flash red. Scott walks into Allison's room and then her bathroom where she's taking a show. Allison quickly wraps the shower curtain around herself, asking Scott to leave. Scott makes no move to do so, stating that he's "seen her naked before." Allison becomes worried because Scott is acting really strange, but just as Scott goes to reach for the shower curtain, he realizes what he's about to do and leaves.
Later, Melissa calls Scott and tells him to look outside. Scott goes to the window and sees Deucalion holding her by the throat and telling him that he's an alpha now. Deucalion then rips Melissa's throat out. Stiles asks if Scott is okay, and Scott looks again and realizes that nothing is there.
Stiles, Allison, and Lydia save the other werewolves from their suicides and then finally find Scott in the parking lot. He’s doused himself in gasoline and is holding the last flare. Scott says that there’s no hope for him or Derek, who he thinks is still dead. Allison tells Scott that Derek wasn’t his fault, but Scott counters that whenever he actually tries to help people just get hurt or get killed. Stiles tells Scott that this isn’t him, but Scott insists that it is. He believes that this is the best thing he could do for everyone else.
Scott talks about what it was like before he was bitten, when him and Stiles were “nothing” and “no one,” and states that “maybe he should just be no one again” before lifting the flare. Stiles steps forward telling Scott that he’s his best friend, his brother, and that he needs him. He steps into the puddle of gasoline around Scott and grabs the flare, telling Scott that, “If you’re going to do this, then, I think you’re just going to have to take me with you.”
Stiles takes the flare and throws it behind him. Lydia notices the flare rolling back toward the puddle of gasoline and runs towards Scott and Stiles, tackling them to the ground as the gasoline ignites.
Coach Finstock gets on the bus in the morning to see Scott, Stiles, Lydia, Allison, Boyd, and Isaac all already on the bus.
Later, Scott brings his mom dinner at the hospital. A women walks up and asks for something for the pain. Melissa turns her away as giving her something could complicate things. Scott then goes to the women and explains that he read somewhere on the internet that human contact can help with the pain. Using his werewolf powers he touches the women lessening the pain. Ethan then comes in carrying Danny Mahealani yelling for help.
Scott and Ethan both seem close to panic as Danny is wheeled into an exam room. Melissa explains that Danny’s heart is being pushed up against his chest cavity. Danny stops breathing, and she jabs a syringe into his left pectoral. Once inserted, needle has a valve that is opened to allow the air to escape and relieve the pressure in his chest.
Scott and Ethan walk outside. Ethan says he didn't do it and tells Scott that the twins were tying to find the person most important to Scott. It wasn't Danny but Lydia. A car rolls into the parking lot. It's Dr. Hilyard's car, the on call doctor, and it's empty. Scott finds a dead and dried moth sits on the seat.
The next morning, Melissa wakes up to find Isaac and Scott sleeping in her room. Apparently while making sure she wasn't the [[human sacrifices+healers|third healer sacrifice], the boys fell asleep.
Deaton calls Scott and tells him that he is the third sacrifice. At the Animal Clinic, Scott tells the Sheriff all he can without revealing his secret. Then he tells Stiles they need to tell the Sheriff. Stiles argues against it, but Scott convinces him that that's the right plan. However, Marin Morell shows up to ask the Sheriff to help find her brother. She then walks up to the boys and tells them that no sheriff or deputy can help find him. She suggests they use Lydia.
Back at the school, while Stiles looks for Lydia, Scott follows a tapping sound to the music room. Duke offers to help Scott find Deaton. Scott is angry, and Duke offers Scott a challenge. If he can get the cane away from him, Duke will tell him where Deaton is. Scott puts up a fight, but loses. Deucalion leaves him with a cryptic clue: "Let the currents guide you."
Scott gets a text from Allison that she found something, and he goes to see her while Stiles, Lydia, and Cora go to the hospital to talk to Danny.
Allison was looking through her father's things when she found a black light. Her father arrives. She herds Scott into her closet. Scott gets an erection. Allison orders him to stop, but he says he can't. The two of them almost kiss when Scott stumbles back, afraid the noise will arouse Chris's suspicion. They hear a door close and exit the closet. They enter Chris's office, and Allison brings Scott over to the map. Scott doesn't see anything until she holds the black light over it. Chris has been tracking and marking everything, the Darach's kills, Cora and Boyd's lock up, the alpha fight. There are more marks on the map than there are sacrifices.
Chris comes back up in the elevator and looks in the various rooms. Scott escapes from behind him.
Scott tells Stiles that Deaton might be at one of the six locations, but they're all over town and he can't get to them fast enough. Stiles tells him that Danny's paper on the telluric currents might have found something.
Scott, Stiles, Lydia, and Cora have met up at the Animal Clinic. They’re going over Danny’s paper and find a map of the telluric currents that run through the ground of Beacon Hills. When they combine Danny’s map with Chris Argent’s map they find likely locations for the future body dumps and figure Deaton is being held somewhere along the telluric current that runs between where he was taken and where his body will be found. Cora realizes the bank where she and Boyd were held is on that current’s path.
Scott heads to the bank to find Deaton. Scott arrives at the bank vault where Deaton is suspended by his arms. Scott rushes forward but is shoved backward with a flash of light. He realizes that Deaton is surrounded by a circle of mountain ash.
Scott tries again to penetrate the force field, pushing against it with all his might and filling the room with a blue glow. His eyes shine yellow then red as he pushes, but the barrier will not bend, and Scott is thrown back to the floor. He looks on helplessly as Deaton hangs there. Sheriff Stilinski is suddenly in the doorway of the vault, gun in hand. He fires at the rope, and Deaton drops to the ground.
Deaton tells Scott about his eyes changing colors. He says Scott is a True Alpha” one who rises on strength of character and sheer force of will as opposed to those who take the status from another alpha. Deaton says it's rare, happening only once in a hundred years but that he believed Scott had this potential in him since he was first bitten.
Scott realizes that this status is what Deucalion has been after: a True Alpha. He realizes that he is the target instead of Derek.
Two days later, Scott and Allison visit Gerard to learn about Deucalion. Gerard turns around in his wheelchair and rolls up his sleeve, asking Scott to give an old man something for his pain. Allison tells Scott that he doesn't have to do this, but it's Gerard price for telling them what they want to know. Scott grips hands with Gerard and starts siphoning away his pain. The pain is intense enough for Scott that his eyes glow.
Gerard tells them that it's interesting that there was another sacrifice so soon after the attempt on Deaton failed. He posits that Deaton is the Darach. Scott is adamant that Deaton would never let anyone innocent die. Gerard tells him that he would be surprised how far some people would go to get rid of Deucalion.
Scott demands to know how to beat Deucalion, and Gerard huffs. "You can't. I've tried." Allison decides that they aren't getting anything out of Gerard, and she tells Scott they should leave. As she's on her way out, Gerard tells her to wait. He tells them that Deucalion may have lost his eyes, but he's not always blind.
He tells them that Talia Hale was a powerful werewolf who could shift into a full wolf. He explains to them the history of werewolves and druids. He reveals the Deucalion wanted to meet with him to broker a peace, but he was sure it was a trap. Scott asks him how he knows they didn't want to make peace, and Gerard replies, "Because I'm not an idiot." Gerard asks if they know the tale of the scorpion and the turtle. It's the same story as The Scorpion and the Frog.
Gerard says that he was ambushed, but Scott doesn't believe him. Gerard asks him to take some more of his pain before they go. He tells Scott that sometimes he wonders what would have happened if he'd done things differently. He wonders when it became his nature to believe that most things couldn't be asked for but had to be taken. Scott replies that he's a really good liar.
Scott grabs Gerard's hand and squeezes hard. He warns him that if he lied and it gets people hurt, he'll be back to take away more that Gerard's pain
Later that week, Scott and Stiles show up late at the school because Lydia called them. She started driving somewhere and ended up at the school, so she's afraid she's going to find a body. Scott finds it instead. Deputy Tara Graeme is dead on the school sign.
At school, Ms. Blake talks about images, analogies, metaphors, and similes. She looks at both Scott and Stiles nervously and then brings up the phrase "seeing the whole board," which Stiles knows refers to chess because his dad plays.
As Ms. Blake moves away, Scott tells Stiles that he thinks he can get to Ethan and make him talk. Stiles wonders why Scott would want to do that. Scott thinks the darach is the emissary for the alpha pack. They decide to separate Aiden and Ethan by having Lydia have sex with Aiden during school.
Stiles and Scott catch Ethan alone in the hallway. He doesn't understand why they're talking to him and makes a threat. Stiles replies in kind. Scott calls Stiles off and explains that they're talking to him because he doesn't think Ethan wanted to kill Boyd and if he had to do it over again, wouldn't do it.
Ethan explains to Scott that the pack they were a part of were killers who gave werewolves the reputation for being monsters. Duke taught them to form Voltron Wolf, and then they killed their pack. Scott asks about their emissary, and the look on Ethan's face tells him that they killed him too.
Ethan gasps in pain, and they realize that Aiden is being attacked. Scott and Stiles go with him and find him fighting Cora. Ethan stops him and nods at Scott as he takes him away.
Cora cleans out her wound while Scott, Stiles, and Lydia watch. She tells them all that she'll heal and tries to stand up straight, but she wobbles and Scott catches her. Stiles calls her crazy, but she accuses them of doing nothing. Scott tells her that they're trying, but she tells him that they're failing.
Scott goes to Ms. Morrell's office and tells her that he could use a little guidance right now. She asks Scott why he's bothering with her when he knows someone else is about to be taken. Scott asks her if she's the one killing people. She tells him to listen to her heartbeat and then whispers, "No. I'm not the one killing people." Scott seems satisified that she isn't lying. She tells him that Deucalion wants to make a killer out of him if he won't join the alpha pack willingly.
When Mr. Westover is taken, Ethan asks Scott what the pattern is, but he doesn't know. Eventually he figures out that it's philosophers, not guardians. He calls Stiles to tell him, and Stiles complains that the teachers are all heading home, so they won't know who to protect, but he's wrong. The teachers will all be at the recital that night. He attends the recital and keeps an eye on the twins. Lydia is there too, trying to use her powers.
When Lydia disappears, Scott and Stiles go looking for her. They don't know where she is until Lydia screams, and every werewolf in Beacon Hills can hear her. Scott goes to find her, but the Sheriff is there first. The Sheriff sees Scott shifted as he attacks Jennifer. Scott spits up blood after one hit and can't keep her from taking the Sheriff. But the time he recovers, they're gone.
Scott and Stiles head immediately to Derek's loft and tell him what happened. When Jennifer arrives, she tries to tell him that the boys will show up and tell him lies, but she quickly realizes that they're already there. Scott accuses her of killing people, and she laughs it off as crazy. She denies knowing where the Sheriff is, and Scott asks her to explain why she almost killed Lydia. Jennifer calls their story absurd.
Scott holds up a bottle of mistletoe and claims it can be either a poison or a cure. He flings a cloud of it at her, and she loses her glamour. Derek grabs her to keep her from running. He starts to strangle her, but both Stiles and Scott beg him to stop. He eventually drops her to the ground.
They all head to the hospital. Stiles thinks something is still fishy because Jennifer didn't look upset that they'd outed her, but Scott isn't sure. When they arrive, he asks Stiles why he has a bat. Stiles points out that Scott has claws and he has a bat.
The run into Scott's mom inside, and she tells them they have to take the last ambulance, which will leave in 20 minutes. Derek ushers Jennifer into the elevator, and Scott and Stiles glare at her, ready to attack if she does anything threatening. They find Cora's room, and Scott sees a trail of black blood leading up the hallway. Peter then comes sliding down the hallway on his back. The twins have formed Volton, and Derek goes to fight them. Scott tries to help. He yells at Ethan and Aiden to stop, but they claim they need to get Jennifer.
Peter and Stiles grab Cora, and they all run. Scott knocks down a lighting fixture into the twins to try to buy time. They stop in an exam room to look for something to fight with, and Stiles yells at Derek. Scott tries to get him to calm down and points out that the twins are still after them. They check on Cora, but Peter says she isn't getting better.
Jennifer reappears and says that Cora won't unless they get Jennifer out of the hospital alive. Derek launches himself at Jennifer, but Scott holds him back. Scott's mom then comes on the loud speaker and says they have 10 minutes to deliver Jennifer. Jennifer assures him that Deucalion won't hurt his mom and Scott knows why. Derek demands an explanation, and Jennifer tells him that Scott will be a true alpha.
Scott decides that they have to get Jennifer out and get Cora to the ambulance. He will distract the twins. Derek wants to stay with him, but Jennifer insists that Derek stay with her. Peter ends up helping Scott. He takes a shot of epi and they run into the hallway to fight them. The others escape to the ambulance but Kali has the keys and Derek can't fight her.
Peter and Scott run, and Peter falls and slides into a wall. He complains that the epinephrine shot didn't last very long as Scott hauls him up. They hide in the laundry room. Scott asks Peter how they're supposed to get past them. Scott then sees the laundry chute. He drops Peter through, and then goes right after, landing on top of him.
Scott gets a text message from Derek. Peter doesn't even have to ask to know that the others didn't get out. Scott texts Derek back not to move and that they're on their way.
Scott and Peter suddenly appear at the window of the ambulance, and Scott orders Stiles to open the door. Peter is crashing so hard that he can barely walk. Stiles hauls Peter into the ambulance and tells Scot that Kali has the keys to the ambulance and the twins are very close by. They both look toward the sound of distant banging, and Scott tells Stiles to stay put.
Scott is in the hallway by himself, listening carefully. He hears something drop, and then the twins attack. They pin Scott up against the wall and demand to know where Ms. Blake is. They claim to be trying not to hurt him. Melissa then hits them with a shock from a crash cart, knocking them apart.
Melissa tells Scott that Deucalion just let her go, but Scott doesn't believe Deucalion would do it without a reason. Scott hears a gun click and comes around the corner slowly to find Chris, Allison, and Isaac.
Chris, Scott, Melissa, Isaac, and Allison discuss Derek and Jennifer being trapped in the elevator. There's no way to get them out without turning the power back on. The problem with that is that the sound of the elevator will draw the alphas to Derek and Jennifer, and they have to avoid fighting the alphas. Scott insists that Jennifer's life is too important to risk because she's their only way to save Stiles's dad and Cora.
Scott texts Derek that they have a plan. Derek opens the elevator doors, making a noise that catches the twins' attention.
While the alphas are distracted by Allison, Melissa turns the power back on. Scott goes to the elevator to find Derek unconscious on the floor and the emergency hatch broken open. Scott realizes that his mother is in trouble and takes off to find her just as Stiles runs up. Stiles calls after him, but he doesn't stop so Stiles runs to catch up.
Scott races to the roof. Deucalion informs him that Jennifer took his mom, a guardian. He makes Scott an offer that if he joins his pack, he will save Melissa. Scott wavers and starts to cry but decides to join Deucalion against Stiles's pleas.
Scott disappears with Deucalion and ends up walking through the Beacon Hills Preserve with him while the alpha pack hunts down Ms. Morrell. Morrell tries to convince him to go back to his friends, but he won't go. The alphas try to kill her, but Scott stops them. In return, she advises him to find the nemeton. Stiles and Deaton call Scott and ask him to meet. They all want to find the nemeton, and they pitch Scott on the idea of the surrogate sacrifice scenario. Scott agrees, although he still plans to side with Deucalion in the fight against the darach.
Scott joins everyone at the Animal Clinic. He's brought his mom's watch with him as a symbolic token of her. When they learn that they will need to have emotional tethers to come back from the sacrifice, Scott and Allison have to address that they are no longer each other's anchors. Deaton ends up being Scott's tether. Just before they're about to go under, Stiles tells Scott that his father is back in town.
Scott, Stiles, and Allison wake up in a white room with the nemeton growing out of the floor. As Scott touches it, he is transported back to the night he got turned. He sees that he was turned near the nemeton. When they all wake up, they learn that they've been dead for 16 hours and it's nearly the lunar eclipse. Ethan shows up asking for their help in stopping Aiden and Kali from killing Derek. Meanwhile, Scott, Isaac, and Allison go to collect personal items to help them track down their parents' scents. They get caught by Agent McCall and are delayed as they try to find a way to get away from him. Among the Argents' things, Scott spots flashbombs and pockets them.
Once they escape, they meet Deucalion at the overlook. Deucalion and Scott go to confront Jennifer while the others look for the nemeton. Scott sends Jennifer a video message of him and Duke at the abandoned distillery. Scott is surprised when Jennifer shows up with Derek at her side and doesn't quite believe that Derek is there trying to help him. Deucalion attacks Derek and Jennifer and then tries to make Scott kill her. Scott refuses and uses the flashbombs to blind Deucalion long enough for the lunar eclipse to hit, so the Werewolf all lose their powers. He lets Derek deal with Jennifer for the length of the lunar eclipse and then attacks her once she has thrown up a mountain ash barrier. Scott pushes through the barrier, becoming a True Alpha when he overcomes her magic.
Scott lets Deucalion slash Jennifer's throat. He and Derek then let Deucalion go with the hope that he will become the good man that he once was.
Scott doesn't want to deal with his father being back in town, and he talks about how he looks to his friends for support now.
A few weeks after they made them sacrifices, Scott, Stiles, and Allison start dealing with the darkness around their hearts. On his way to school, Scott sees a shadow of his hand with claws out, even though he hasn't shifted. It's symbolic of his fear that he will become a monstrous, out of control alpha like Peter had been. Isaac talks to Scott about liking Allison, and Scott hits him out of jealousy. At school, Scott continues to have problems knowing if he's controlling his shift. He meets the new girl, Kira, and likes her right away. At one point, he starts to shift in the middle of the hallway, and Stiles pulls him into an empty room. Scott digs his nails into his hands to cause himself pain so he will remain human.
Later, they all sit outside and discuss the weird things that have been happening to them. Kira stops by to tell them about bardo. Scott and Stiles go to the clinic to talk to Deaton about what's happening, but he doesn't have any good advice.
The Sheriff has been looking at all his old cases now that he knows about the supernatural. He asks Scott to help him investigate a girl who went missing from a car crash 9 years ago. Scott agrees and breaks into the Tate's house to look for a scent, but it's too long ago and he can't get anything.
Scott has a confrontation with his dad, who is trying to get the Sheriff fired. He nearly loses control and shifts, but his mom advises him to be his own anchor. That night, he and Stiles go to check out the car crash site themselves and find claw marks on the car.
Scott takes off after Malia, chasing her through the woods. They find her den and Scott suggests calling in the Sheriff to investigate. The Sheriff isn't sure that they've really found Malia, but Scott is convinced that she shifted on the full moon and caused the car crash. They ask for Allison's help in tracking her down, but she isn't much help.
In class, Kira gives Scott research that she did on bardo and is embarrassed by her father, who makes it clear that Kira likes Scott. Stiles is asked to read in class, but he can't because he's lost the ability to read. He starts to have a panic attack, and Scott hurries him to the bathroom. He talks Stiles through it, asking how you know if you're dreaming. Stiles is convinced that they can't do this, but Scott tells him that they have to try.
Kira gets attacked by Malia, and Scott saves her. He learns more about Kira and about the fact that she has trouble making friends. Stiles admits that he took a doll from the car crash and that now it's missing from his bag, which means Malia took it. They want to hunt her down and gets some tranqs from Dr. Deaton. Scott thinks he can make Malia shift back into a human because Peter once made him shift with just his voice. The problem is that Scott has alpha performance issues. Derek isn't answering his phone, and they don't trust Peter, so they end up asking the twins for help on being alphas. The twins mostly just beat Scott up without being able to force him to use his powers.
They chase Malia through the woods, and Scott ends up stopping her by the car crash site. He alpha roars, forcing her to change, and they return her to her father.
Scott meets Stiles at the school on Mischief Night to set up a prank for Coach. The next day, Ethan and Aiden ask to join his pack, which Stiles finds hilarious. Scott refuses because he doesn't trust them. Scott continues to show interest in Kira and Stiles encourages him to go for it. He hears her tell her dad that she doesn't need a boyfriend and looks let down. Eventually Stiles finds Scott and tells him that William Barrow, the shrapnel bomber, escaped and is in the school. Scott has his mom bring some of Barrow's clothes, so he, Isaac, and the twins can search the school themselves.
Before they can find anything, Stiles pulls the fire alarm, and they all leave the school. Scott heads over to Kira's house because her dad invited him over for dinner. They think that Scott will be very cultured because he lives in California, but he's never had sushi. Kira feeds him some. He learns a little about their family and the fact that Kira comes from a very important lineage.
Kira ends up buying pizza for them, since the sushi wasn't a hit. As Scott is leaving, Barrow hits him with a tire iron and takes Kira. He wakes up to Stiles and Lydia standing over him. They figure out that Barrow is at the power station and head there. Scott attacks Barrow but gets hit with a power line and goes flying. He watches as Kira absorbs all the electricity.
Scott, Stiles, Lydia, and Kira get taken to the sheriff station to talk about what happened at the power station. He asks Scott what he and Kira were up to, and it sounds like they're lying when they say they were having sushi/pizza for dinner. Rafael lets them go but warns Scott about the seriousness of lying about something like this.
At school the next day, Scott wants to talk to Kira about what happened, but she avoids him. Stiles thinks this is wise. Scott finds her in the hallway eating lunch by herself and sits with her. She has him take her photo with his phone so he can see her aura and then admits that Barrow took a photo of her with her phone, which is why she wants it back from the police. Scott gets Stiles to help them break into the sheriff station. They sneak in and have to charge Kira's phone in order to delete the photos. They barely make it out without getting caught.
Scott then invites Kira to the black light party Danny is throwing. She's uncomfortable but goes. Stiles goes too and tries to tell Scott about the mysterious key that's on his keyring, but Scott isn't too concerned. He spots Allison at the party and gets distracted, but eventually focuses on Kira. When he uses his alpha vision, he can see her aura. They go up onto the roof to sit and talk.
Scott hears Derek howl and realizes that he's back. Derek throws everyone out of his loft, and Scott and Kira come down to see there are Oni in the place, going after Aiden. Scott places himself between the Oni and Kira, but the sunlight through the window wipes the Oni away before they can do anything else.
When Scott brings Kira home, she asks him to shift so she can see his wolf face. He does, and she touches him gently.
Scott goes to talk to Chris about their encounter with the Oni. After he hears about the encounter, he goes to school, where Ethan and Aiden have decided to act like bodyguards. Stiles tries to show him the chemistry lab and the writing on the board that led Barrow to Kira, but the extra key is gone and so is the writing. Scott is adamant that Stiles wouldn't have been involved. At the end of the day, Scott ditches Ethan and Aiden and takes Kira to his house. They talk about whether the Oni are out to kill Kira. They look at a children's book of kitsune tales, and Scott almost kisses Kira, but they're interrupted by Scott's dad.
Scott dismisses his dad's accusations that he broke into his office. While they're fighting, the Oni appear. Derek busts into the house, having followed Scott all day. The twins appear also, and then Melissa closes a mountain ash circle around the house, keeping the Oni out. Rafael is hurt badly, but they don't call anyone because it might just get more people hurt.
Kira is sure that the Oni are out to get her, but Scott assures her that she isnt' evil. He gets a call from Allison advising that he let the Oni perform their test. Scott tells everyone to stand down, and he and Kira get their Oni marks. When they take Agent McCall to the hospital, Scott learns that Stiles is there and finds him wandering around. He didn't see him take on the Oni.
Scott wakes up to his cell phone ringing. Stiles tells him that he's trapped and doesn't know where he is but he's afraid and needs to be found. Scott shouts for Isaac, and they start searching for him. They go to Stiles's room to get something with his scent on it but find Lydia already there. Lydia tells the Sheriff that Stiles is missing, launching a search. They find his Jeep at the hospital and head there. Scott goes up on the roof, where Derek has already followed Stiles's scent. Derek teaches him to read emotions in scents, and they realize how terrified Stiles is.
Lydia uses her powers and is led toward Eichen House, so they get the Sheriff to look for him there, but the basement they look in is empty.
Melissa and Rafael McCall find him instead, and everyone meets at the hospital. Stiles is fine from his ordeal, so everyone goes home. Scott heads back, however, when they're going to do an MRI. Stiles is exhibiting the same symptoms as his mother. Stiles and Scott talk about it, and Scott says that if it comes down to it, he'll do something to help him. The implication is that he'll give him the Bite. They hug while crying. While Stiles gets scanned, Scott sits in the hallway with Derek. They talk about Scott being the one who has to look out for Beacon Hills. Derek's family used to protect it, but he's going to just be a mentor for Scott now. They realize that Stiles was trying to protect them all from himself and rush up to the roof in time to see a power line break.
Scott and Derek rush down from the hospital to see Isaac get electrocuted and Kira absorb the electricity from the power line. When Scott visits Isaac in the hospital later, he finds Allison sleeping in the hallway because they won't let her in. They go in together and Scott takes some of Isaac's pain while vowing that they'll figure out how to save Stiles. Kira tells Scott that the nogitsune must be very offended to be this violent.
The twins continue to act as bodyguards. They hear a sonic emitter in the basement of the school and all go down to find Stiles. Scott stops the twins from hurting him, and Stiles shows them all the gear he has, even though he doesn't know what he's been doing with it. They find a map of the cross-country trail and the places Henry Tate set out steel-jaw traps. They rush to the trail to make everyone stop running, fear that the traps have been moved to the trail. Coach gets shot with an arrow, and Scott draws out some of his pain. He does this again when a bomb goes off in the sheriff's office, taking the pain from a dying man. He and Stiles run to the Animal Clinic to find a safe place from the Oni, but Scott gets stabbed. Once they're inside, Stiles twists the sword, making it clear he's the nogitsune. The nogitsune draws all the pain that Scott had absorbed throughout the day out of him. Deaton appears to inject the nogitsune with letharia vulpina and then removes the sword from Scott's stomach.
When Scott hears that Stiles is being put into Eichen House, he races to catch up with them. He argues that he can't help Stiles if he's locked up, but Stiles insists and Scott has no choice but to watch him go in. Scott then joins up with Allison, Lydia, and the twins on a plan to rob an armored truck to get the shugendo scroll that Katashi owned, which is supposed to contain information on stopping the nogitsune.
Scott thinks the plan is terrible, but they don't have a better one. Kira shows up and demonstrates her katana skills to Scott so he'll let her come on the heist. The heist goes awry because Kincaid got there first. Scott isn't able to fight him, but the twins can. Scott does keep them from killing him, though, because they've gotten the scroll.
Kira and Scott confront Noshiko Yukimura after having a look at the katana and photo that Malia brought them. They learn that the woman in the photo who looks like Kira is Noshiko herself and that she's 900 years old. She explains that there was a massacre at the Oak Creek internment camp and she summoned a nogitsune to seek revenge on those who perpetrated it. Only the nogitsune didn't possess her, it possessed the body of her dead lover. She tells them that they can't stop the nogitsune or save Stiles, but Scott refuses to believe her.
The Sheriff, Derek, Chris, and Allison are at Derek's loft with the nogitsune. Scott and Kira races to meet up with them, but they're too late. They go back to Scott's house, and he lets Kira take the bed. She doesn't want to be alone, though, and they kiss. The next day, Lydia and Aiden find Stiles in a parking lot and bring him to Scott's house. They keep him immobile with kanima venom.
Scott, Lydia, and Deaton discuss whether giving Stiles the Bite would solve their problem. Scott doesn't want to without knowing that Stiles would be okay with it. He also doesn't know if there's something more involved and calls Peter for advice. Peter advises against the Bite and instead has Scott use his claws to send him and Lydia into Stiles's mind to try to set him free. Inside Stiles's mind, Scott is distracted by thoughts of Allison, until he hears Peter yelling from the real world. Then he breaks the illusion and ends up in the white room with Lydia, where they can see Stiles at the nogitsune on the nemeton. They try to run to him but can't. Lydia tells Scott to call Stiles like he's pack. He howls, and Stiles dashes the Go board in front of him away.
They come out of the vision and watch as the nogitsune starts spewing up bandages. Scott and Peter tackled the person that looks like the nogitsune as it crawls from the floor, but Scott realizes first that it's not fighting them. He takes the bandages off to reveal Stiles. The nogitsune takes off with Lydia, and Scott races out the door calling her name.
Stiles insists on having Noshiko's Oni check him to be sure he isn't still possessed. Scott isn't pleased but watches him go through it. He then takes Stiles to go see his dad, who hasn't been privy to anything that's gone on since the Derek's loft. They don't know what the nogitsune would need with a banshee, but Stiles suggests that they ask Meredith Walker, someone he suspects of being another banshee. Meredith ends up at the school, so Scott and Stiles go there to get her. They bring her back to Scott's house, where Rafael is waiting.
While Stiles deals with Meredith, Scott has to talk to his father. His dad explains how he knocked Scott down the stairs once during a drunken rage and Melissa threw him out. Scott doesn't really care to hear it. He responds that getting hurt happens all the time around their house. He's more angry about his dad being gone than the fact that he was physically hurt.
Scott, Isaac, Kira, and Stiles head to the Oak Creek internment camp to face the nogitsune. They meet Allison there. Scott tries to give them a pep talk about finding Lydia, which largely falls flat because no one was questioning that they were going to try to save her. Scott and Stiles leave Isaac, Allison, and Kira to face the Oni and the nogitsune. During the fight, Allison dies protecting Isaac. Scott comes out of the compound to catch her as she falls. She dies in his arms.
Scott can barely concentrate as Chris tells him how to talk to the cops about Allison's death. He lets Isaac do the talking at the station. He and Lydia then talk to Deaton about the fact that it was the nemeton keeping the nogitsune captive. Deaton reveals that the triskele urn that houses Talia's claws is made out of nemeton wood and could contain the nogitsune. Stiles and Kira arrive, and they all head to the school to enact their final plan.
Scott swears to Stiles that the only plan he's going through with is the one where Stiles lives, even though Stiles is willing to sacrifice himself to end it all. When they go into the school, they enter the garden in Japan where the nogitsune was stabbed by the Oni. The nogitsune tells them that Scott must assist Stiles in committing suicide. Scott won't. He and Kira prepare to fight. Stiles grabs a sword and threatens to kill himself. Scott yells at him to stop but does not physically stop him. When Stiles realizes it's all an illusion, he tells Scott to just walk out of the room. Scott walks the gauntlet of Oni cutting him up, but when he emerges, they all escape the illusion.
In the days that follow, Scott mourns Allison's death and helps Malia Tate learn to control her transformations.