Stiles is asleep in his room, squirming restlessly with a nightmare. He whimpers and repeats, "No no no, don't let them in." Bars of light start to shine across his face, and he wakes up suddenly trapped inside a locker. It's difficult to tell if he thinks he's lying down or standing up. He beats the door open and stumbles out into the boys locker room at school. As he wanders the halls, he's drawn to an open classroom. The nemeton is growing through the floor of the room, and the light outside cartwheels. Stiles slowly reaches for the nemeton, and as his hand gets close, tendrils of wood snake out and wrap around his arm. He gasps awake. "You okay?" Lydia asks, in bed next to him. He looks down at his arm and then sighs. He tells her he was just dreaming. He says it was weird, like a dream within a dream. He grasps her hand for comfort as she rubs his shoulder, and then he realizes that something is wrong. "Wait a sec, Lydia, what are you doing here?" Before she can say anything, the door to his room opens on its own, and Stiles is pulled to investigate it. Lydia asks him not to go, but he says he's just going to close the door. She tries to stop him from getting out of bed to close it, but he insists. He worries about someone coming in. Lydia's pleas get more desperate as he grabs the door knob and pulls the door open. He walks through and out into the woods with the nemeton. Stadium lights turn on, illuminating everything, and a high wind blows. "This is just a dream," Stiles tells himself. "Wake up, Stiles. Wake up!" He clutches his head and pulls at his hair. Stiles wakes up peacefully to the sound of birds chirping. Sheriff Stilinski opens his door and tells him it's time to get up for school. Stiles sighs.
Scott and Stiles are talking at school. Stiles tells Scott that he couldn't wake up and it was beyond terrifying. "You ever hear of sleep paraylsis?" He explains that this happens during REM sleep because your body is basically paralyzed (muscle atonia) so you don't start running for real because you're running in the dream. But sometimes your mind can wake up before your body does, so you're aware that your body is paralyzed. "And that's the terrifying part," Scott concludes. Stiles agrees that it turns dreams into nightmares. Stiles asks Scott if making themselves into sacrifices is still affecting them. Scott asks if he means PTSD. They get to class, and Stiles says, "You want to know what scares me the most? I'm not ever sure this is real." He bolts upright in bed screaming. His father comes running into the room and practically tackles Stiles into a hug. The Sheriff pulls Stiles into his arms and holds him while he screams. "Hey, hey, hey, it's okay, you're okay," he says, as Stiles clutches at his arms, crying.
Scott gathers his books for school, and when he turns to leave, he notices his shadow cast against his bedroom door. His human hand is casting a shadow with werewolf claws. Scott checks his hand to confirm that he hasn't shifted, but the shadow remains. Scott closes his hand, and when he opens it again, the shadow is normal. He opens the door and finds Isaac just about to knock. Isaac asks if Scott is going to school, and when Scott says yes, Isaac tells him that he's also going. He seems anxious. Isaac asks Scott if he's angry at him, and Scott says he isn't. "Are you sure?" "No." Scott confesses that he's not really sure how he's feeling. Isaac asks if he hates him, but Scott says no. He asks if Scott wants to hit him, and Scott denies that as well, but Isaac suggests he hit him anyway. Scott doesn't want to. "You didn't do anything, did you?" Isaac asks Scott for clarification, and Scott asks him if he kissed Allison. Isaac didn't, so Scott asks if he wanted to. "Oh, yeah, totally." Scott throws Isaac into the wall in the hallway. Melissa comes up and tells them not to test her totally unsupernatural level of patience. She motions for them to get to school, and Isaac asks Scott if he feels better.
Stiles throws his books into his bag, but stops when he realizes that he can't read the title of one of them. Dalesi Xis Anla it says. Stiles stares at the book and touches the cover with shaking fingers. His father comes in and asks him if he's all right. Stiles looks back at the book, and this time the cover says Allies and Axis. Stiles says that he's good a little too quickly, and his father gives him an incredulous look. Stiles insists that he's fine and it was just a nightmare. Stiles then asks his father about the box of case files he's carrying, which is marked "Sheriff's Station: Do Not Remove." "Well, yeah, unless you're the Sheriff," his father replies with a grin.
Allison grabs her purse as she hurries out the door. She gets in the elevator, but when it opens, it lets her out into an abandoned hospital hallway. She steps out into the hall. Momentarily, a second Allison wielding ring daggers appears in the background, but vanishes. The door to the morgue opens on its own, and she goes inside. The door closes behind her, and one of the freezer doors swings open, beckoning her to come look. The tag on the door says Kate Argent. Allison hears her aunt's voice and remembers both their good times and when she saw Kate murdered. She looks in the freezer, and it's a tunnel that goes back impossibly far. As she peers down the shaft, something starts moving. Kate is suddenly clawing her way toward Allison, screaming in rage. Allison slams the door shut and runs. When she bursts through the morgue doors, she's at school just as the bell rings, utterly bewildered as to how she got there. She stares around in shock, and Lydia comes up to her and asks her if she's okay. Allison nods unconvincingly.
Scott arrives at school on his dirt bike. He takes off his helmet and looks down at his reflection in the visor. His eyes in the reflection glow red, even though Scott's eyes are not. He shakes himself, and the vision goes away. As he walks into school, Scott turns and notices his shadow growing and morphing into the same monstrous shape that Peter took on when he was an alpha. Scott starts to run, but he can't escape his own shadow. He crashes into Stiles, who tells him he doesn't look all right. Scott claims to be okay, but Stiles knows that none of them are. When Scott asks how he knows, Stiles motions to Lydia as she and Allison walk up. "Because it's happening to all three of you," Lydia says.
In his office, Sheriff Stilinksi has started going through all his old cases. Now that he knows about the supernatural, he wants to see if he can solve any crimes that previously went unsolved. He has marked out all the nights with full moons on the wall and put up strings to try to make connections. He pins a photo of Malia Tate up on a night of the full moon.The props department hasn't been paying attention to what year it is, because the Sheriff has calendars from 2013 up on his wall. The Sheriff remembers the car crash where Malia's family died.
Lydia leads the other three into the school. "Well, well, look who's no longer the crazy one," she says, clearly enjoying being on the other side of the terrifying visions for once. Allison complains that they're not crazy, but Lydia snarks and disagrees. "We did die and come back to life. That's gotta have some side effects, right?" Scott says. The bell rings, and they all head to class. Stiles tells Lydia to stop enjoying this so much.
There's a new history teacher, Mr. Ken Yukimura. He says his family moved to town three weeks ago and mentions his daughter Kira. He says she's never mentioned anyone from school or brought home a friend. Kira sighs and slams her head down on the desk. When her father points her out, she looks around at everyone with an embarrassed smile. Scott gives her a lingering look and a small grin. The are learning American History at the turn of the 20th century. Scott sees his shadow, and it again starts growing into a monstrous alpha.
Allison is having a difficult time in Art class. They're painting, but she can't keep her hand steady. Lydia comments on it, and Allison says it's been happening for the past few weeks. Allison throws the brush down in frustration, and red paint splatters on the canvas. It reminds her of Kate's blood splattering on the window when Peter cut her throat. Lydia tears the canvas off and orders Allison to start over. She watches Allison closely. Isaac also watches from across the room.
Stiles goes to his locker and tries to open it. Scott suggests that maybe they just need a little more time to get back to normal. "Try not to forget that we hit the reset button on a supernatural beacon for supernatural creatures. I think there's a pretty good chance that things are never going back to normal." Stiles struggles with the combination lock. All the numbers have turned into alchemical symbols.
Scott overhears Kira and her father arguing. He thought she wanted him to point her out in class so she'd be noticed. She says she could set herself on fire and be noticed, too. Kira catches Scott look at her, and he quickly turns away, but something about their interaction set Scott off. His eyes start to glow. Stiles notices and hugs Scott to his chest to hide his eyes from others. Kira notices them make an escape. They rush into a classroom, and Scott starts to shift the more he freaks out. Scott orders Stiles to stay back because he can't control himself. When Scott's claws come out, he digs them into his palms, making himself bleed. He fights the shift and ends up collapsing with the effort. He pulls the transformations back, and Stiles looks at his bloody hands in concern. "Pain makes you human," Scott says in a shaky voice, remembering something Derek once taught him. Stiles tells Scott that this isn't just in their heads. "I'm not just having nightmares. I'm having these dreams where I have to literally scream myself awake. And sometimes I'm not even sure if I'm ever actually waking up." Scott asks what he means. Stiles explains that in a dream you can't read, and he's been having trouble reading more and more the last few days. Scott asks if it's happening right now, and Stiles looks at the blackboard. It's covered in gibberish.
Lydia is still determined to help Allison somehow. They go to the woods, and Lydia sets up an archery target on a tree. She tells Allison to shoot a few arrows and see what happens. Allison misses by a wide margin every time. Lydia suggests trying a Mongolian draw. Allison does, but the results are the same. Lydia asks Allison to close her eyes and imagine the arrow going to the target. When Allison opens her eyes, she sees Kate running through the woods. She tells Lydia to wait there and goes off to follow the vision. Allison doesn't go very far, but suddenly she doesn't know where Lydia is and hears Kate calling her name. She turns and continues to see Kate running through the trees. Allison spins, and it's suddenly night. She knocks an arrow, and the corpse of Kate comes at her. Allison fires. Isaac catches the arrow before it goes into Lydia's face. It is daylight again. Allison is stunned and drops her bow.
Later, Isaac reports to Scott that Allison almost killed Lydia and that she keep seeing her aunt. "Whatever's happening to you guys is getting worse." If Isaac hadn't followed them to the woods, then Lydia would be dead. This prompts Scott to ask him what he was doing there. Scott doesn't like the answer and throws Isaac into the wall again.
Stiles goes to meet his dad at the sheriff's station. He has flowers for his mother's grave and complains that the last time they left her flowers someone stole them the same day. His dad tells him that it's not the flowers, it's the gesture. Stiles sees his father's case files spread all over the place and asks what he's up to. The Sheriff explains that he's going through all the old files looking for any he might be able to solve now. Stiles reads a file about a bipedal lizard report, and his dad tells him to toss it on the kanima pile. The Sheriff says there are at least a hundred cases where he can ask himself "If I knew then what I know now..." Stiles isn't sure this is a healthy thing to do. His father says there's one case in particular that's been plaguing him. Eight years ago when he was elected sheriff of the county, his first official duty was to tell a man that not only had his wife and two kids died in a car accident, but that as best they could tell the body of his 9-year-old daughter had been dragged from the wreck by coyotes. They hadn't found the car until three days after the crash. The two bodies that were still in the car were covered in bites and slashes. Stiles concludes that the bites and claw marks now make him think werewolf attack. But he points out that coyotes could actually be the culprits. The Sheriff agrees, except the accident occurred on a full moon, which makes it suspicious. Stiles then asks where all the case files are going, and the Sheriff tells him that Rafael McCall has asked for them all because he's trying to impeach him.
The next day, Stiles goes to Business class and finds someone sitting in his normal seat. He asks her to move, but she responds to him in sign language. He lets her keep the seat. As he opens his textbook, he notices that the rest of the class has gone very quiet and still. Coach Finstock stands at the front of the class with a blank expression. He starts signing the same thing that the girl did. Stiles tells him that he doesn't know sign language and is surprised that the Coach does. Freaked out, Stiles decides to leave. When he looks back at the classroom, everyone is doing the same sign, faster and faster. Stiles backs up and looks like he's having a panic attack. He holds his head in pain. And then it becomes clear that the sound he's hearing is the Coach's whistle. Stiles startles awake in his seat. Finstock yells at him that he asked him a question. Stiles asks him to repeat it. "It was Stilinski, are you paying attention back there?" "I am now," Stiles replies. Scott looks at Stiles with worry. Stiles tells him that he's okay, he just fell asleep for a sec, but Scott tells him that he didn't fall asleep. He glances meaningfully at Stiles's notebook, and Stiles looks down to see that he's written "wake up" repeatedly.
During a free period, Allison, Isaac, Lydia, Stiles, and Scott sit outside and talk about the situation. Scott asks what happens to a person who has a near death experience and comes out of it seeing things. "And is unable to tell what's real or not," Stiles adds. "And is being haunted by demonic visions of dead relatives," Allison says. Isaac quips that all those people are locked in asylums for being insane. Stiles asks him to be helpful. "For half my childhood I was locked in a freezer, so being helpful is kind of a new thing for me," Isaac replies. Stiles tells him to stop milking that excuse. Kira appears at their table and says that she overheard them talking about their symptoms. She says that it sounds like they're talking about bardo, the in between state between life and death. They all sort of stare at her. Lydia asks her what she's called. Scott supplies that her name is Kira, and they grin at each other. Lydia asks if this is bardo in Tibetan Buddhism or Indian. Kira replies that it's both. All the things they described happen in bardo. There are states where there are hallucinations, some you can see, some you just hear. "And you can be visited by peaceful and wrathful deities." Isaac asks what the wrathful deities are, and Kira says they're demons. "Demons! Why not..." Stiles replies. Allison asks what the final state is if bardo has progressive states. Kira tells her you die. None of them look very happy.
Stiles and Scott go to visit Deaton. He tells Stiles that his subconscious is trying to communicate with him. "Well how do I tell my subconscious to use a language I actually know?" Stiles asks. Deaton has him repeat the signs and translates, "When is a door not a door?" "When the door is ajar," Scott supplies. Stiles in incensed that his subconscious is telling him riddles. Deaton says it's not necessarily a riddle. When the three of them sacrificed themselves, they opened a door in their minds that is still ajar. Scott asks what they do about it, and Deaton tells him that's difficult to answer. Stiles says that Deaton's face has the "we know exactly what's wrong with you and no idea how to fix it" look. Deaton tells them that they each need to close the door in their minds.
The boys leave the Animal Clinic, and the Sheriff drives up. He asks them for help, specifically Scott. He wants Scott to try to get Malia's scent and find her body, which could provide him the clue he needs to close the case. Stiles asks what happens if it was a werewolf, and his dad replies then that means there's someone out there who murdered an entire family and needs to be caught.
The Sheriff goes to visit with Henry Tate, who explains that he's been having a coyote problem as he unboxes a have-a-heart trap. The Sheriff comments that the trap looks too small for a coyote, but Henry Tate says that traps are for the rats that the coyotes come to eat because if you take away their food source they leave you alone. "These days, to be honest, I prefer to be left alone," he says pointedly. The Sheriff promises he only has a few questions. While he's talking to Henry Tate, Scott and Stiles sneak in the back door. Stiles starts offering Scott items from the room to see if he can get Malia's scent. "All I'm getting is some animal smell," Scott says. Stiles asks what kind, and Scott stops dead at the sound of a growl. "Dog." A rottweiler stands in the room looking at them. Stiles tells Scott to get rid of the dog, but Scott doesn't know how. Stiles tells him to glow his eyes at it and act all alpha-ish, but Scott won't because he's not sure he can control himself. The dog, Apollo, starts barking at them, and Henry Tate yells at it to shut up. Eventually the dog leaves, listening to its master. Scott can't pick up any scent other than the dog. Stiles spots a photo of Malia and her sister and snaps a copy of it. Henry Tate is distraught at the Sheriff's suggestion that his family was murdered. He's spent 8 years accommodating the idea that it was a tragic accident, and he doesn't want to entertain the possibility that someone actually wanted them dead. He orders the Sheriff to leave, and the Sheriff realizes what a mistake his reopening the case might be. He meets up with Scott and Stiles, and Scott apologizes for not being able to get a scent. The Sheriff tells him it was a terrible idea anyway. "I think I just ripped a wound open in that poor man. I never should have brought you guys here. I don't know what I was thinking." After the Sheriff leaves, Scott asks Stiles if there are a lot of cases that go unsolved. Stiles tells him there are, but his dad thought maybe he could figure this one out right now. Scott asks why it's so important now, and Stiles explains about the impeachment investigation.
That night, Scott argues with his dad. He tells his dad to get out of the house. His dad tells him that he's just doing his job. Melissa comes home and asks what's going on. "He's trying to get Stiles's dad fired." Agent McCall denies that but then tells Melissa that he's conducting a case for impeachment. Melissa backs up Scott, but Agent McCall says that a lack of resolution and inability to close cases is going to be what gets him fired. Scott's anger starts to take over, and his claws start to come out. Melissa sees his hand and pulls him away quickly, telling him to breathe and let the anger go. Scott's eyes glow, and his teeth come out, despite his efforts. Melissa tells Scott to find his anchor, but Scott tells her that his anchor was Allison. Without her, he doesn't have one. "Be your own anchor," Melissa advises. Scott fights and gets his transformation under control. Melissa then tells him that even though it doesn't feel like it, he's going to fall in love again. And it will be just as magical and amazing the second time. But until that happens, Scott needs to be his own anchor. Scott heads over to Stiles's house and gets him out of bed. He says they're going find a body: a dead body, echoing the series premiere.
Allison is in bed, with Isaac kissing her neck. She asks if Scott's okay with this, and he replies that Scott's 100% over it. She asks again to make sure, and Isaac assures her that Scott's moved on so she should too. Isaac sits up to take his shirt off, and Allison runs her hand up his chest. She frowns at him and asks what's around his neck. He feels for the cord wrapped around his throat, and it suddenly tightens. Kate appears behind him, pulling the garrote. "Let's do him, Allison," she says. "Let's do him together." She jerks the garrote tighter, and Allison finds a ring dagger in her hand. She gasps awake. She and Lydia fell asleep while studying. Allison lies back down and finds something digging into her back. She pulls out a ring dagger.
Stiles and Scott are in the woods. Stiles points out that if his dad's right then there's another werewolf in town they haven't met. He says if they're triplets that transform into Cerberus, he's really not up for that. Scott's not up for any unfriendly werewolves either, since he can't control himself. They hear a coyote howling, and Stiles grabs onto Scott, making him drop his phone down an embankment into a pool of water. Scott retrieves his phone, which still works. Stiles grabs the flashlight from Scott and hurries ahead. They've found the car crash. Scott is surprised the wreck is still there and not hauled away as evidence. Stiles suggests that the inaccessibility of crash probably made them decide it wasn't worth the trouble to find a way to get it out. The inspect the car and find claw marks on the door that are too wide apart to be an animal's paw. It's looking more and more likely that a Werewolf attacked the vehicle. They look inside the car and find the doll that Malia was holding in her photo. Stiles pulls it out, and they both stare at it. "I'm hungry!" the doll says, making Stiles scream. Scott hears growling and sees blue eyes shining in the darkness nearby. Scott takes off after the creature. He leaps over a ravine and lands coming face to face with it. It looks more like a coyote than a wolf. It snarls at him, but Scott glows his eyes red back at it, and it calms down. Its eyes glow blue in response. "Malia?" Scott asks. And then the creature runs away.
A number of bloodied instruments are lined up on a table, along with a cell phone. It's Derek's phone, and it lights up with texts from Scott asking him to call back because they need help. Derek and Peter, however, are chained to a metal fence being electrocuted. Derek glares at Peter. Peter asks him why he's looking at him like this is his fault. "Because it is your fault." Peter agrees that he's probably right.