The film starts with an obituary for Ellen Leigh, who is survived by her daughter Annie Graham (Toni Collette) and her grandchildren. Annie attends her mother's funeral with her husband Steven (Gabriel Byrne) and their kids Peter (Alex Wolff) and Charlie (Milly Shapiro). Annie gives a eulogy for her mother, pointing out that there are people there that she doesn't know and that Ellen was into things that Annie knew little about.
The Graham family lives somewhere in the woods. Annie designs scale models based on things she is familiar with, like her home life or her taking care of Ellen on her deathbed. Steven gets a phone call informing him that Ellen's grave has been desecrated, but he doesn't tell Annie. She goes to tuck Charlie to bed, where she mentions to her mom that Ellen had always wanted Charlie to be a boy. Afterwards, Annie goes into her workshop where she finds a note from Ellen stating that she is sorry for whatever she feels happened between them, but ends with a promise that the rewards will be worth it. Annie thinks she sees some kind of figure hidden in the shadows, but after turning on the light, she finds nothing.
Annie attends a grief counseling meeting after telling Steven she is going to the movies. She explains to the group what kind of person Ellen was, in that she suffered from Dissociative Identity Disorder, and how her father died when she was a baby while her brother was schizophrenic and always accused Ellen of trying to put people in him before he eventually killed himself.
At Charlie's school, a bird hits a window during a test. After class, Charlie swipes a pair of scissors and cuts the bird's head off. She brings it home and makes a doll with it. In her room, she notices a blue flash of light surrounding her. She then walks outside and sees what appears to be Ellen surrounded by flames before Annie scolds her and pulls her back into the house. Peter asks Annie if he can borrow one of his parents' cars to go to a party, and Annie makes him take Charlie with him.
At the party, Peter leaves Charlie alone while he goes to smoke weed. She eats chocolate cake with nuts in it and she begins to suffer an allergic reaction before going into anaphylactic shock. Peter rushes Charlie to the hospital, and she opens the window to stick her head out and breathe better. Peter sees an animal on the side of the road and swerves hard, causing Charlie's head to hit a telephone pole, decapitating her. Peter sits in shock and silence before driving home slowly and quietly going home. The next morning, he hears Annie's blood-curdling scream as she discovers Charlie's headless body in the car. We even get a gruesome look at her severed head on the side of the road as it is being devoured by ants.
Annie becomes detached and inconsolable after Charlie's death, avoiding Peter and even sort of hating him. Peter himself is wracked with guilt to the point where he suffers a painful physical reaction at school while smoking weed with his friends. He even appears to hallucinate seeing Charlie in his room, down to hearing the tongue-clicking sound she would always make. Annie returns to the support group and then meets a woman named Joan (Ann Dowd), who invites Annie to speak with her because she knows what it is like to lose a child.
Annie visits Joan's apartment to talk. She reveals to Joan that she sleepwalks and once had an incident in which she doused Peter and Charlie with paint thinner and lit a match, leaving them both horrified even as Annie tried to convince them that she was only sleepwalking. Joan also explains how her son and grandson drowned months earlier.
At home, Annie continues making her models, but she has created one of the accident in full detail (with blood and everything). Steven finds her and scolds her for it, hoping that Peter will not have to see it.
The family sits down for dinner, which goes well until Annie and Peter start arguing, with both of them hurling insults at one another and essentially blaming each other for what happened to Charlie.
Annie visits Joan again to see that she is conducting a seance to speak to her grandson Louie. Annie is shocked to discover Joan is telling the truth when the force in the room causes a glass on the table to move, and then it starts to write on a chalkboard "I love you Grandma".
Annie later sleepwalks again and has a nightmare that she walks into Peter's room and blurts out that she never wanted to be his mother and that she tried to miscarry. It ends with them covered in paint thinner and being set on fire. She wakes up and grabs Charlie's sketchbook to perform a seance. She wakes up Steven and Peter to prove that she is telling the truth. The presence in the room moves a glass on the table and also manipulates the fire on a candle. Annie then starts speaking like Charlie, wondering what is going on until Steven splashes her with water to snap her out of it.
Peter hallucinates seeing Charlie again. He then feels hands pulling on his head, and when he wakes up to see Annie, he accuses her of doing it, but she denies it.
Annie believes Charlie's spirit is angry, so she throws the sketchbook into the fireplace, but her arm catches fire, and she has to pull it out to make it stop. She then goes to find Joan, but her apartment is empty. Upon returning to her house, Annie goes to the attic where she finds a swarm of flies everywhere. She finds what appears to be her mother's headless corpse in the corner, along with a symbol drawn in blood on the wall above the body. Annie then looks through an album in a box to find pictures of Ellen and, to her surprise, Joan engaging in some kind of ritual. Annie looks through another book to find a description on a demon named Paimon who desires the body of a human male as a vessel.
During lunch, Peter sees Joan across the street yelling "I expel you" to him, but nobody else appears to notice her. He also notices the same blue flash that Charlie saw earlier. In class, he sees his reflection grin at him. Peter's face and body then start to twist unnaturally before he smashes his face into his desk and breaks his nose. Steven has to go pick him up.
Steven confronts Annie over what is going on, and tells him what she found in the attic. When Steven sees Ellen's body, he believes that Annie is the one that desecrated her grave and dug up her body. Annie begs Steven to burn Charlie's sketchbook to stop everything, but he refuses to keep listening to Annie. She throws the book in the fireplace after dousing it with lighter fluid, and then Steven's whole body goes up in flames. The blue flash appears and overtakes Annie.
Peter wakes up in the middle of the night. He doesn't see Annie crawling on the walls behind him. He goes downstairs and finds his father's charred body. Annie then attacks him and chases him to the attic. Peter finds his grandmother's body. Annie is levitating on the ceiling as she starts to cut her head off with a wire. He sees nude old people that are part of Ellen and Joan's cult, and, now completely freaked out, Peter jumps out the window to his apparent death.
The blue flash then takes over Peter's body and he appears to regain consciousness. He goes to the nearby treehouse where Joan and the other cult members are waiting for him. He sees a statue with Charlie's decomposed head mounted on it and with a crown on top, right next to a picture of his grandmother with "Queen Ellen" written above it. Joan speaks to Peter, addressing him as Paimon and saying that they have succeeded in providing him with a body after he had been using Charlie's body as a vessel. The cult bows to Paimon as they worship him.
*CUT TO THE CHASE*
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Annie Graham's mother Ellen passes away after a lifetime of having a strained relationship and no idea what Ellen was really into. Soon after, Annie's daughter Charlie dies in a freak accident, causing Annie to blame her son Peter because he was driving the car when Charlie was killed.
Annie encounters a woman named Joan who helps her perform a seance to contact Charlie, only for supernatural events to plague the family. It is soon revealed that Ellen and Joan were part of a cult that tried to summon the demon Paimon into the body of a male in the family, but he had previously settled in Charlie's body, so nearly everything that happens to the Graham family was orchestrated by Ellen and Joan.
After Annie attempts to get rid of the hauntings, her husband Steven is burned alive, and her own body gets briefly possessed to kill herself before Peter jumps out a window to his own death. Paimon uses this as an opportunity to take over his body and join the cult where they bow to him.
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