The year is 1941 in London. The Blitz of World War II has happened. Men, women, and children are hiding underground. A young schoolteacher, Eve Parkins (Phoebe Fox), walks out into the streets to see the wave of ruin left over the city.
Eve meets with her associate Jean Hogg (Helen McCrory) and a group of children. Jean tells Eve that a boy named Edward (Oaklee Pendergast) has lost his parents and his home during a bombing. The boy is brought to Eve, and he doesn't speak a word. The group boards the train to go to the countryside and stay in a home to take care of the children. During the ride, a military pilot named Harry Burnstow (Jeremy Irvine) gets in the car with Eve and introduces himself. He presents himself in a charming manner toward Eve and the kids.
The group arrives at a village. They come across an abandoned home. Eve enters and encounters a blind man that mutters something to himself. He frightens Eve and sends her away. Next, the group comes to the Eel Marsh House. Jean is displeased with the state of the home, thinking it to be unfit for children to occupy. Still, everyone settles in. Eve makes sure Edward is comfortable, but he still won't speak.
At night, Eve has a vision of herself walking through a hole in the wall that leads her through a hospital room. The beds and floors are covered with hair shavings. She walks past a woman holding a baby, and another woman screaming. Eve spots a crib and walks over to it. She tries lifting the blanket and has a hand grab her face. She wakes up from this and finds herself walking into the basement. It's dark and quiet. She sees a writing on the wall that reads, "You let him go".
The other children play together while Edward stays in the room to draw. Eve tells two boys, James (Pip Pearce) and Tom (Jude Wright), to include Edward in their activities. The boys go into the room and approach Edward. Tom grabs his drawing and tells him he'll give it back after a game of Hide and Seek. Tom makes Edward cover his eyes while he counts. Edward goes looking for the boys and walks into a room where Tom locks him in. Edward tries to get out and knocks loudly, alerting Eve. From behind him, the boy sees a dark figure. He sits in stunned silence before Eve comes up and opens the door. She finds Edward simply staring up at the wall.
Tom continues to tease Edward by keeping his picture. While the children sleep at night, Tom gets up and walks out of the house. The next day, Jean and Eve frantically search for him and see that the front door was unlocked. Eve runs to the beach to find Tom lying dead in the sand. The ladies group the children and tell them to stay together at all times. Eve talks to Edward and asks if he saw anything. He hands her a note that says, "She told me not to tell." Eve questions him more and he hands her another note that says, "You let him go."
Eve goes for a walk through the area and finds a tombstone for a child named Nathaniel Drablow. In the distance, she spots what seems to be a figure. She chases after it but loses the figure.
Eve calls Harry and tells her what happened with Tom. He comforts her and helps her investigate. Harry finds a recording of a voice describing the events prior to the death of Nathaniel Drablow. The speaker claims to have seen the ghost of a woman right before the boy drowned. As they further investigate, Eve finds a note from a woman named Jennet Humfrye, who wrote to Nathaniel before his death, saying that she was his real mother. The boy died two days after she wrote it.
A girl named Joyce (Amelia Pidgeon) notices that Edward has the drawing that Tom took from him. She questions how Edward got it, but the boy pulls it away from her. Later, Joyce sees red string going from the stairs to another room. She pulls it off and walks into the room. She sees the ghostly figure and starts to wrap the string around her neck. Downstairs, Eve is in the basement and is encountered by a blind man like earlier. He starts saying a little rhyme about his friends having eyes and how they died. He tries to lock Eve down there, but she escapes. Jean finds Joyce before she finishes strangling herself.
The group comes together in the wake of this incident. Eve then tells Harry that she once had a child, but he was taken from her after his birth, and Eve never got to see him again. She thinks that Jennet's ghost is trying to take Edward from her. Jean dismisses Eve's claims and thinks she is responsible for poisoning the children's minds with fear. The lights then flicker and go out. Joyce walks upstairs without being noticed. She enters a room and puts on a mask, suffocating herself before anyone can find her. The adults then find the child dead.
The group leaves the house and Harry takes them to a military air station for safekeeping. They are unable to leave as the planes are fake and the base was meant to be bombed by the Germans as a decoy. Harry admits to Eve that he was demoted after an incident where his crew was killed. He considers himself a failure as a pilot and a man. Eve comforts and kisses him.
Before the group can get to bed, the ghost terrorizes them yet again. They hold hands and repeat a saying to themselves while closing their eyes to not give the ghost any attention. She shrieks frightfully, terrifying everyone. Edward leaves the base and Harry runs after him, just as the fire baskets start going off. He thinks he spots Edward in one of the fake planes, but it is the vision of a ghoulish child. Harry then finds Edward running toward a pit with a fire basket. The boy falls in and the fire basket explodes. Harry returns to the base with the boy's shoe. Eve breaks down in tears.
Eve later notices Edward's drawing and sees a face in the house he drew, next to a woman and a child. She realizes the boy is still alive, and she runs back to the house. She is unable to catch Edward as he runs toward the lake. The ghost traps her in the house, but Eve breaks through the floorboards and runs after Edward. The boy is walking deeper into the lake toward a cross. Eve calls out to him and reminds him of a phrase he wrote to her about bringing down bad dreams with good thoughts. Edward snaps out of it and moves toward Eve. A pair of hands start grabbing the two of them and pulls them further down into the lake. They struggle to break free until Harry jumps into the lake and pulls Eve and Edward up to the surface. He stays behind and is pulled into the depths of the lake by the hands, allowing the two to escape. They get back to the shore, and Edward finally speaks, telling Eve, "I'm sorry."
Following the end of the war, Eve has become Edward's guardian. He is dressed up and ready to go into town with her. After she fixes him up, she looks up at something with a sad expression. The two of them leave, and the camera pans back into the house to show what Eve was looking at - a picture of Harry and his crew members. The frame breaks as we get one final look at...THE WOMAN IN BLACK!
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