The film is set in the fictional town of Gatlin, Nebraska, an agricultural community surrounded by huge Cereal#Farming. In 1980, The town appears to be neglected, except for the church, and residents choose Biblical names over more modern ones. When the corn crop fails one year, the townsfolk turn to prayer to ensure a successful harvest. However, 12-year-old (he was 9 in the book on which this film is based) Isaac Chroner takes all of the children in Gatlin into the cornfields and indoctrinates them into a religious cult based around a bloodthirsty deity called “He Who Walks Behind the Rows”. Isaac and his subordinate, 18-year-old Malachai, lead the children in a revolution, murdering all of the adults (ages 19 and up, since 18-year-olds are seen as halfway between teenager and adult) in town as human sacrifices. Only Job and his sister Sarah refuse to participate, as they can see visions of the future, drawing them on paper.
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, intending to 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 He Who Walks Behind the Rows, the demonic entity the cult worships.
Eli and Joshua are being taken into foster care with William and Amanda Porter of Chicago after the death of their father, who was killed by Eli. The two boys do not mix well with a home in modern Chicago; their formal, Amish-like clothes from Gatlin and Eli's fire-and-brimstone prayer at dinner, as well as his bringing a suitcase full of corn to Chicago, strike their new parents and neighbors as unusual. On his first night in Chicago, after everyone else has gone to sleep, Eli quietly leaves the Porter's house for an empty factory on the other side of a nearby cornfield. Taking with him the suitcase of corn, Eli prays to "He Who Walks Behind the Rows" and plants corn seeds on the grounds of the factory, causing rows of corn to appear almost instantly.
Grace Rhodes is a medical student who returns to her hometown of Grand Island, Nebraska, to take care of her agoraphobic mother, June (Karen Black), who refuses to leave her yard. She is having recurring nightmares of being attacked by children. Grace also has to look after her younger siblings James and Margaret. She takes a job at Dr. Larson's local clinic, where she'd worked prior. James and Margaret become ill and show symptoms similar to those of the children in June's dreams. The next day, while working at Dr. Larsen's office, Grace notices that many other kids have the same symptoms. During the night all of the kids in town get worse as their fevers skyrocket. Suddenly it all stops and the fevers begin to drop.
A group of teenagers become lost in middle America and arrive in Divinity Falls, where forgotten children have taken on the duty of serving "He Who Walks Behind the Rows". The teenagers have less than a week to get out of the town. However, they find that their car is destroyed, and the children are held accountable. Alison, the leader of the teenagers, overhears that the children are the adopted wards of Luke Enright, a madman who considers himself the savior of the children, and the earthly representative of He Who Walks Behind The Rows. Upon remembering that her brother is also among them, Alison and the rest decide to go to Enright's farm to discover the truth behind the bizarre cult.
Hannah, the first child born of the original Gatlin corn cult, visits the town of Gatlin to find her real mother. On the way, she picks up a street preacher by the name of Zachariah whose car broke down. He tells her about her name, and then vanishes. After crashing into a corn field a lady sheriff suddenly appears and takes Hannah to a hospital in town. Once there, she finds out Isaac was not killed by "He Who Walks Behind The Rows" after the death god took control of his body in the first film, but instead went into a coma. The hospital appears to be filled with strange patients who speak of a prophecy involving Hannah and Isaac before the scene changes.
Jamie (Claudette Mink) comes to Omaha, Nebraska after numerous phone calls to her grandmother have gone unanswered. Her grandmother's apartment building, which is built next to a cornfield, appears to be empty, except for two young, mysterious children who roam about. Jamie discovers that her grandmother has received a notice of eviction. She goes to see Det. Armbrister, who is not much help. While at the local grocery store, Jamie has an encounter with the children from the building, but they do not speak to her. Outside, she sees a priest standing in the street, staring at her. She returns to her grandmother's apartment to discover a message: "Jamie go home."
In 1963, the town of Gatlin, Nebraska, is suffering a severe drought. In a tent,
Tim and Allie's car breaks down and they attempt to find shelter in a remote desert farmhouse after becoming lost. A strange Charles Manson-like character, Preacher (Billy Drago), allows them inside to use the phone. The couple find out they won't be able to get tow service until the following day. Preacher and his Ukrainian wife Oksana also known as Helen let them stay the night with strict orders to be gone by morning, and not wander "where you are not invited." They find their hosts weird but don't think much of it and head to bed after dinner. Allie wanders off in the middle of the night after using the outhouse, and discovers the garage has been converted into a cult worshipping church. She then stumbles upon a crumbling outbuilding where she hears faint cries coming from a child.
