In Northern California, 2007, a woman attends a rehearsal dinner for a wedding. There, she tells the story of an au pair, which dates back to 1987 in London. American native Dani Clayton is hired by Henry Wingrave to look after his niece and nephew in their manor in Bly. Dani arrives with Owen the cook and meets the children, Miles and Flora; the housekeeper, Hannah Grose; and the gardener, Jamie. Flora warns Dani not to leave her room at night, but Dani ignores this. She finds many talismans spread throughout the manor, one of which belongs to the previous au pair, Rebecca Jessel, who allegedly killed herself. Hannah describes the talismans as a protection for Flora. She sees a man on the parapet. When Dani stumbles on The Lady of the Lake's talisman, she is locked in Flora's cupboard by Miles. She sees a spectre she has seen repeatedly in a mirror in the closet. Dani is let out a few hours later and notices muddy footsteps. When she follows them outside, she sees Miles and Flora staring at her from their windows.

Dani tells the children that while she forgives them for locking her in the closet, she does not believe their story. In a flashback to his days in prep school, Miles exhibits increasingly erratic behavior—picking fights, killing small animals—and he is expelled. It is suggested that Miles wanted to be expelled, as he holds a letter from Flora that says "Come home." In the present, Dani makes the children do the house chores, giving Hannah and Jamie a break. Dani has a panic attack when Flora tries on a pair of broken glasses she finds among Dani's things. Miles acts unnervingly adult-like toward Dani, which creeps her out. While playing a game of hide-and-seek, she discovers a photo of Rebecca and her lover. Her lover is the same apparition she saw on the parapet, and he appears again. Miles falls unconscious and the ghost grins eerily at Miles.

A flashback to a year before reveals that the ghost whom Dani saw earlier is Peter Quint, who works with Henry and meets Rebecca Jessel when she interviews for the au pair position. They begin a relationship. Flora gifts Rebecca the doll she made of her. Peter becomes possessive of Rebecca and jealous of Rebecca's interactions with Owen. The photo that Dani found is revealed to have been taken by Peter in the off-limits wing of the house, and that Hannah disapproved of their relationship. In the present, the police fail to find Peter on the grounds. Assuming Peter is alive, the adults deduce that Peter may not know Rebecca is dead and may be stalking the grounds. Flora is found by the lake in the morning, staring at Rebecca's ghost. At story time, Miles presents a story about puppets who forgot their maker and mocked him. They receive a call and learn that Owen's mother has died. Dani has a panic attack once again and screams as she sees the same spectre appear before her.

In flashbacks, Dani is engaged to her childhood friend Edmund. One night during a date, Edmund realizes Dani does not want to marry him and the two fight in the car. As Edmund exits the car angrily, a truck runs him over and kills him. A traumatized Dani sees Edmund's spectre for the first time at the hospital and plans to leave the country without telling anyone. Edmund's mother gives Dani Edmund's glasses before she leaves. At Bly Manor, Dani joins the house staff at a bonfire after Owen's mother's funeral. Jamie initiates a traditional remembrance of the deceased, "throwing bones into the fire", but Dani does not participate. Dani and Jamie fall in love. Dani later awakens in a drunken stupor, but Flora notices the faceless doll in her dollhouse. The children prevent her from seeing a white-clad female spirit wandering the manor. After putting the children to bed, Dani burns Edmund's glasses.

Hannah flashes back and forth between events at different points in time, some real and some imaginary: the day she interviewed Owen for the cook position; the night of the bonfire when he offers to take her to Paris; and the time of Rebecca's employment at the manor, when Hannah caught Peter stealing from the Wingraves. One night, Peter is killed by the "Lady in the Lake", the faceless white-clad ghost who tracks mud into the house. Reincarnating as a ghost, he discovers he can possess Miles. Hannah sees Miles speaking to Peter. Peter then possesses Miles and shoves Hannah down the well, killing her. Dani arrives at the manor after, revealing that Hannah was killed right at that moment and has unwittingly been a ghost since Dani's arrival. The episode ends at the bonfire, where Hannah agrees to go to Paris with Owen, only to see him toasting her goodbye as he leaves with Jamie.

Flashbacks reveal that Henry was having an affair with his brother Dominic's wife Charlotte before their deaths and is Flora's biological father. After deducing this, Dominic cuts ties with Henry, reasserting himself as Flora's father and forbidding Henry to contact the family. Dominic and Charlotte travel to India in an attempt to save their marriage, but are killed there in an accident. In the present, Henry drinks heavily and refuses to answer Dani's calls when Flora behaves strangely and sleepwalks. At night, he calls the manor hoping Flora will answer but hangs up when anybody else does. Flora repeatedly "dream hops", flashing back to the past in dreams about Charlotte and a faceless boy ghost in her room. She speaks to Rebecca's ghost, who visits her at night and is the cause of these occurrences. Dani ends up seeing Rebecca and Peter's ghosts. As she tries to flee with Flora, Miles knocks Dani unconscious.

In flashbacks, Peter learns the mechanics of being a ghost at Bly Manor; he is able to possess the living temporarily, but can do so permanently if he is invited. If a ghost remains in Bly Manor for too long, they will lose their face along with their sense of self. As a ghost, Peter convinces Rebecca they can be together forever if she invites him to possess her. Rebecca agrees but Peter walks into the lake in her body, drowning her and rendering her a ghost as well. Rebecca is horrified and feels betrayed but Peter convinces her that using the same method, they can permanently possess Miles and Flora, letting them start new lives together. In the present, the two ghosts and the children take Dani to the attic while the ghosts enact their plan. The children let the ghosts possess them permanently. When Hannah calls out to them, Peter, as Miles, leads her to the well where he killed her, forcing her to accept that she is a ghost. Flora reveals that she and Rebecca only pretended to carry out the possession and Rebecca's ghost is still separate. Dani once again attempts to escape with Flora but is attacked by the Lady in the Lake.

Centuries ago, the owner of Bly Manor, Willoughby, dies, orphaning his two daughters, Viola and Perdita. Viola marries their distant cousin, Arthur Lloyd, to Perdita's chagrin, who has feelings for Lloyd. After having a daughter Isabel, Viola falls ill with a lung disease. She refuses her last rites, insisting she "will not leave". She becomes bitter and angry as her disease worsens, and she is isolated from the family, frequently searching for her daughter. Perdita, no longer able to tolerate her sister's worsening condition, smothers Viola to death and marries Arthur herself. Viola's spirit is trapped in a chest in the manor, filled with dresses and jewelry she bequeathed to Isabel. Arthur's finances dwindle and, at risk of losing the house, Perdita opens the chest, hoping to sell Isabel's inheritance to keep them afloat. Viola's spirit kills Perdita. Finding Perdita's corpse, Arthur fears the chest is cursed and sinks it into the lake on the property before leaving with Isabel. Viola becomes the Lady in the Lake, searching the manor for her daughter at night, and killing anyone in her path, as well as trapping those who die on the grounds. Her memory fades along with her face over the centuries.

As Viola drags Dani by the throat, she is intercepted by Flora. Flora reminds Viola of Isabel so she takes Flora to the lake to drown her. Dani saves Flora by letting Viola's ghost permanently inhabit her body, releasing all the previously trapped souls that had died in the house over the centuries. Henry returns to Bly Manor to raise the children as his own; Owen and Jamie find Hannah's body in the well. Dani and Jamie leave for America to start a life together. After five years, Dani starts to see Viola's reflection and worries her appearance may harm Jamie. During their visit to Owen's restaurant in France, he reveals that Flora and Miles do not recall the events at Bly Manor and only have happy memories. Dani wakes one night with her hand around Jamie's neck. Not wanting to risk Jamie's life, Dani returns to Bly Manor and drowns herself in the lake, taking Viola's place. The storyteller, now revealed to be a middle-aged Jamie, ends the story and enjoys the wedding reception of a now grown-up Flora, with Miles, Owen, and Henry. Back in her hotel room, Jamie waits by the door, hoping to reunite with Dani's ghost, who watches over her as she falls asleep, with a hand on her shoulder.