The film starts with the same opening scene from The Conjuring, in which two young women and a young man in 1968 are telling Ed and Lorraine Warren about their experience with a doll they believe to be haunted, known as Annabelle.
One year earlier in 1967, John and Mia Gordon (Ward Horton and Annabelle Wallis) are expecting their first child. John gives her a doll that she apparently has been trying to find. Mia loves it and puts it with the rest of her doll collection in their baby's room.
At night, Mia hears a murder happens at the Higgins', their neighbours, home. She tells John and he goes over to investigate. He runs out of the neighbor's house covered in blood (not his), telling Mia to call the police. She does and is about to head back outside when she is attacked by a woman with Mia's new doll and the male murderer. John and the police arrive and kill the man while the woman kills herself in another room. She left a bloody symbol drawn on the wall while holding Mia's new doll. A drop of her blood falls on the doll's face and sinks into its eye. A news report is shown that the assailants were Annabelle Higgins and her boyfriend. They murdered her parents and are said to have been part of a satanic cult.
The doctors say that Mia's baby is fine but there was damage to her cervix. She is ordered to stay bedridden for the remainder of her pregnancy, so John takes care of Mia as she recovers. Thinking the doll is creepy and involved with the mysterious happenings, Mia asks John to throw it away. He dumps it in a bin outside. Later, a fire starts by itself in the kitchen, before Mia finally notices. She tries to run out of the house but is dragged by an unseen force and she falls on her stomach. A group of men run into the house and pull her out. John, who works at the hospital, runs to find Mia. She is unharmed, and what's more, she gave birth to a healthy baby girl. They decide to name her Lea. The family moves into a new apartment since Mia is afraid to return home. In their new place, Mia unpacks her dolls and finds that the new doll that was thrown out, now known as Annabelle, in one of the boxes. Mia just places it alongside the other dolls. As expected, more strange activity plagues Mia and her new baby.
Mia contacts the detective that told them earlier about the murders Annabelle and her boyfriend committed. He informs her of their history in the cult called The Disciples of the Ram that seeks to summon a demon by claiming a soul. This also explains the symbol that Mia keeps seeing. Mia goes to a bookstore run by a woman named Evelyn (Alfre Woodard). She gets a book called "The Devil's Welcome". From that, Mia determines that the presence that is haunting her wants a soul - Lea's. The couple contacts their church's priest, Father Perez (Tony Amendola). He takes Annabelle (who looks more gray and scary with bloodshot eyes) with him to church. The ghost of Annabelle is nearby, along with a demonic-looking creature. Perez enters the church but is blown back by a powerful force and is thrown on his back. He is injured, and the ghost snatches the doll. John treats Perez at the hospital while Mia meets with Evelyn. Evelyn tells Mia that she had a daughter named Ruby that was around Mia's age when she died. Ruby died in a car accident caused by Evelyn. She was so distraught and guilt-ridden that she attempted suicide by cutting her wrists. However, she claims to have heard Ruby's voice telling her that it wasn't her time.
Perez warns John that it was indeed Annabelle's spirit that caused his injuries, and that she will take a soul that night. John rushes to warn Mia. In the apartment, the demonic presence haunts Mia and Evelyn. It pushes Evelyn out of the apartment and taunts Mia by locking her outside of Lea's room where the baby sits beneath the bookshelf. The demon thretens to kill Lea for her soul, before Mia attempts to kill Annabelle and it turns into a dead Lea, then another one of Mia's giggling dolls. The demon then asks for Mia's soul instead after Mia screams for what it wants from her. John runs home as Evelyn is trying to open the door. They both break it open to find Mia ready to jump out the window with Annabelle in her hands. John pulls Mia back in before she jumps, saying there must be another way. Evelyn grabs Annabelle and decides to make the sacrifice, knowing this is the way she can atone for Ruby's death. She plunges out of the window and hits the pavement. Lea is found heard in her crib, safe and sound. John and Mia mourn for Evelyn as they embrace their daughter.
Six months later, the Gordons have moved on and have not seen Annabelle since then. Elsewhere, a woman (the mother of one of the girls in the opening) comes into a store looking for a present for her daughter and ends up purchasing Annabelle. The ending text states that the real Annabelle doll resides in a case in Ed and Lorraine Warren's little museum,which is the opening scene of The Conjuring; and that it's blessed by a priest twice a month. A quote from Lorraine Warren states that evil is real, and while we can contain it, we can never get rid of it. The film ends with the camera lingering on Annabelle as though she'll make a move, before cutting to black.
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