An unidentified young woman's corpse is discovered half-buried in the basement of a house marked by a gruesome and strange murder scene. A police officer concludes that there are no signs of forced entry, indicating that the victims were attempting to flee the residence instead.
Small-town coroner Tommy Tilden and his son Austin, who helps him, are in the midst of performing an autopsy on a burned body when Austin's girlfriend Emma arrives, intrigued by the bodies in the morgue. As she spots a bell tied to one corpse's ankle, Tommy elaborates that such bells were historically used to signal if someone was merely comatose rather than truly dead. Soon after, Sheriff Burke (Michael McElhatton) delivers the enigmatic body and insists that Tommy determine the cause of death by morning. Though Austin had plans for a date with Emma, he chooses to help his father, agreeing to meet her afterward.
Since the victim's identity remains a mystery and her fingerprints are absent from police records, she is referred to as Jane Doe. The autopsy begins, but an external examination reveals no visible signs of trauma—her corpse appears unsettlingly fresh, despite the cloudy eyes indicating she has been dead for several days. Furthermore, her wrist and ankle bones are shattered without any observable injuries, and her tongue has been non-surgically severed.
Delving deeper during the internal examination, they are startled as the radio randomly shifts channels by itself. When Tommy incises her chest, blood pours out unnaturally, a phenomenon typically seen in fresh corpses. He attributes the corpse's oddly small waist to the use of a corset, common for women in earlier times. Austin soon notices that the blood he had stored in the freezer is leaking in a strange manner. Upon examining her lungs, they discover they are charred, consistent with someone who has suffered from severe burns. The autopsy reveals numerous internal cuts and scarring, suggesting prolonged violence.
As eerie sounds resonate from the airshaft, Austin investigates and finds their injured cat, Stanley, inside. Compassionately, Tommy puts Stanley to rest by ending his suffering and cremating him. In a shocking discovery, they find Jimsonweed in Jane Doe's stomach—a paralyzing agent predominantly found in the northern regions. Despite hearing about an impending storm, Austin is eager to leave, but Tommy insists on finishing their work.
Their investigation progresses as Tommy discovers a missing tooth wrapped in cloth within Jane Doe's abdomen, containing Roman numerals, letters, and a drawing. Upon further exploration of the corpse's skin, they are stunned to find similar symbols inscribed within. Suddenly, an explosion of lights plunges them into darkness, and they realize the storage chambers are now empty, the corpses that once lay there vanished.
In a panic, they attempt to leave only to find the elevator non-functional, and something obstructing the exit door. Communicating with the sheriff via landline proves futile, and a bell tolls ominously in the hallway, suggesting the movement of the very living corpses they dread. In an attack, Tommy sustains injuries from an unseen entity, merely catching a fleeting glimpse of its grey eyes.
Their decision to cremate Jane Doe leads to unexpected complications when the autopsy room locks itself, trapping them. After Austin breaks through a door with an axe, he is horrified to glimpse one of the living corpses. They try to set Jane Doe ablaze in the examination room, yet the fire spreads chaotically and consumes the recording camera. Despite extinguishing the flames, the corpse remains unharmed.
As they race to the elevator, they are met with calamity when the door fails to close properly. Frantic and desperate, Tommy strikes at a pursuing figure with an axe, only to realize too late that it is Emma, fatally wounded in the fray. Her loss shatters Austin's spirit, leaving Tommy filled with remorse.
Finally realizing that Jane Doe's body hinders them from uncovering the truth, they resolve to re-enter the examination room. In a haze of smoke from the cremation furnace, Tommy is violently assailed. Against all odds, they return to the examination room, and upon opening the skull, make an unsettling discovery: the brain tissue is inexplicably active.
The evidence suggests that a formidable force is preserving Jane Doe’s life. As patterns from the Bible emerge—connected to witchcraft through the mention of Leviticus 20:27—Austin deduces she must be a witch from the Salem trials. However, Tommy contends that the women accused then were victims of mass hysteria and that the terrors inflicted upon Jane Doe may have transformed her into the vengeful spirit she is now.
In a sacrificial act, Tommy offers himself to the witch in hopes of shielding Austin, as her body mysteriously begins to heal while Tommy endures the same brutal injuries she suffered. Stricken with anguish, Austin kills his father to end his torment. As the lights flicker back to life, Austin hears an illusory call from the sheriff outside, prompting him to ascend the stairs, only to be confronted by the apparition of his deceased father.
In a tragic misstep, he stumbles backward over the railing, succumbing to fatal injuries. The following day, law enforcement arrives to a crime scene that defies explanation; with the radio announcing an unprecedented sequence of sunny days that starkly contrasts the chaotic events of the previous night, they find no sign of forced entry.
In the end, Jane Doe's body, devoid of any autopsy evidence, is taken to another county. As she is transported, a faint twitch from her toe suggests that her torment might not be over, each timid movement accompanied by the haunting sound of a bell.
