In a Waco, Texas, diner, Cadillac Jack's, crazed killer Millard Findlemeyer opens fire on the Leigh family, killing Jeremy and James, but leaving Sarah and her mother, Betty, alive. Findlemeyer is arrested and sentenced to die in the electric chair. After the execution, Findlemeyer is cremated, and his ashes are sent to his mother, a witch who mixes the ashes with a gingerbread spice mix. The Bakery, a pastry shop run by the Leighs, is in dire straits, and Betty has been reduced to a shotgun-toting alcoholic; Sarah sends her home with Bakery employee Julia. Jimmy Dean attempts to buy Sarah out, so he can knock down The Bakery, which he bemoans as an eyesore. After exchanging hostilities with Dean's daughter Lorna, Sarah defers the decision.
Sarah and Brick Fields, another Bakery employee, find a mysterious gingerbread spice mix left at their doorstep by Findlemeyer's mother. They set to using the mix, but Brick cuts himself, unknowingly allowing his blood to pollute the dough. Sarah permits him to leave early so he can pursue his amateur wrestling career as The Butcher-Baker at Wrestlepalooza. She makes a large gingerbread man with the contaminated dough and puts it in an industrial oven to bake. Lorna has returned and planted a rat in The Bakery so the health department will shut them down, but is discovered by Sarah. A fight ensues, during which Lorna hits a switch that causes a surge of electricity into the oven where the gingerbread man is cooking, animating it.
Amos Cadbury, Lorna's boyfriend, who has gotten tired of waiting outside for her, arrives on the scene. Sarah removes the gingerbread man from the oven, at which point the newly dubbed "Gingerdead Man" leaps up, taunting them. They attempt to lock the living cookie in the freezer, and Sarah tries to call the police but the line is dead. Lorna calls her dad on Amos’s cell phone before the batteries go dead. Betty comes back to look for her stash of alcohol, and Julia comes back looking for Betty. Betty loses a finger and is put into the oven, while Julia is knocked out by a frying pan, encased in frosting, decorated, and left in the freezer.
Amos returns to his car and retrieves a handgun. Jimmy Dean arrives to pick up Lorna. While he investigates Amos’s car, the Gingerdead Man takes Jimmy's car and, using a rolling pin to operate the accelerator, kills him by pinning him between the car and a wall. Amos and Sarah discover and rescue Julia from the freezer. Sarah tells Amos that she thinks the killer cookie is Millard. Lorna waits outside for her father, but discovers only his body sprawled over the hood of his car. She steals his ring and heads back inside, where she triggers a tripwire that lodges a knife into her forehead, killing her.
Sarah and Amos admit their feelings for one another before they find Betty and attempt to rescue her from the oven, but the Gingerdead Man locks Sarah in the oven and knocks Amos out with a hammer. Amos recovers, shoots the oven door's lock off, and saves Sarah. Brick returns to help, but the Gingerdead Man grabs Amos's pistol and opens fire. Julia and Brick manage to subdue him, and Brick eats the cookie's head. Shortly afterwards, Brick is possessed by the Gingerdead Man. He attacks Sarah before she is rescued by Amos and Julia, who push Brick into the oven and turn the heat on full, finally killing him.
Several months later, Betty, Sarah, and Amos are having a bake sale to raise money for the hospital, with a little help from two nurses. Two kids ask if they have any gingerbread cookies, and one of the nurses tells them that an older lady stopped by and dropped some off. The nurse opens the box, revealing five gingerbread cookies, who open their eyes. One of the gingerbread cookies is bought by a woman, who also buys a box full of pastries and ships them to her sister in Los Angeles.
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