The plot involves the dark goings-on in Hemingford, Nebraska, a town near Gatlin, the original film's setting. The people of Hemingford decide to adopt the surviving children from Gatlin and help them start new lives. Unfortunately for the well-meaning locals, the children return to the cornfield where one of the cult members, Micah, is possessed by a demon sent by He Who Walks Behind the Rows, the demonic entity the cult worships.
Caught in the middle are city reporter John Garrett and his son Danny, who are having a bitter falling-out over John's failed relationship with Danny's mother. John is in town working on a story about the children to save his downward-spiraling career. He runs into two of his former coworkers, Bobby Knite and fellow reporter Wayde McKenzie, who are on their way out of town. Later they are killed in a nearby cornfield after taking a shortcut in their van; a mysterious, powerful storm that lasts only minutes causes the surprisingly-sharp cornstalks to wreak havoc. Back in town, John meets bed-and-breakfast owner Angela Casual and they soon become lovers. Looking to distance himself from his father, Danny befriends orphaned local girl Lacey, who tells him some disturbing details about Gatlin.
Micah and the other children murder local woman Ruby Burke by sabotaging the hydraulic jacks supporting her house while she is underneath it, causing it to descend and crush her. Micah then kills another townsperson in the town, David Simpson, during church services with a knife and a wooden voodoo doll, which causes him to bleed to death from his nose. John starts to question the town doctor about what is going on, but the doctor acts suspiciously and asks John to leave. The doctor is later stabbed to death in his office by the children. Micah and the children later kill Mrs. Burke's sister, Mrs. West, in the road and make it look like she was struck by a car.
John partners with Frank Red Bear, a professor at a nearby university, to make sense of the recent chaos and death. They discover that certain residents are selling spoiled corn from the previous year's harvest along with the new crop. Growing on the spoiled corn is a dark-green acidic toxin which they believe is filling the town's air and contributing to a spate of delusions in the children, rendering them emotionless and violent. The Sheriff discovers them spying on the site of his (and the dead doctor's) misdeeds, ties them up, and tries to kill them with a corn harvester, but they escape.
The Sheriff and the rest of the Hemingford adults attend an emergency town-hall meeting to discuss the situation, but the children lock them inside and set the building afire, killing them all. The children then kidnap Angela and Lacey and take them out to the cornfield where they pressure a confused Danny to join them in sacrificing Lacey. John and Frank arrive driving the harvester. One of the children shoots Frank with an arrow, wounding him. Danny and John free Lacey and Angela and attempt to escape but the cornfield seems endless and they shortly return to where they started. Micah attempts to harness the power of He Who Walks Behind the Rows until Frank restarts the harvester, before he dies. Micah's robe gets caught in the machine and he calls for help. His face transforms, first into the demon that possessed him, then back to himself. Danny runs in to help him but is too late. The harvester pulls Micah in, killing him. The rest of the children scatter, and Danny, Angela, Lacey, and John leave the clearing.
John and Danny later reconcile as they burn Frank's body and give him a funeral before they, Angela, and Lacey drive off together, presumably returning to the city.
Some unspecified time later, it is revealed that Frank's spirit has become the protector of Hemingford.
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