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, Eli's fire-and-brimstone prayer at dinner, and them 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 Porters', taking his corn-filled suitcase, and heads to an empty factory on the other side of a nearby cornfield. There he prays to "He Who Walks Behind the Rows" and plants corn seeds on the factory grounds; rows of corn appear almost instantly.
The next day the boys start school, and Eli nearly gets into a fight with T-Loc, a student in Joshua's grade, and harshly criticizes Joshua for playing basketball with some of the other students. Disgusted with their classmates' modern lifestyle, Eli decides to bring He Who Walks Behind the Rows to Chicago, which soon kills a homeless man who finds the cornfield. Joshua makes friends with neighbors Maria and Malcolm and spends less time with Eli.
The social worker who brought Eli and Joshua to the Porters' discovers that Eli was originally adopted from Gatlin, Nebraska (the town from the first film) and that he has not aged since 1964. She tries to warn the Porters, but Eli quickly burns her alive. Amanda notices Eli's strange mannerisms, and when she tries to cut down his cornfield it attacks her. She attempts to escape, but she trips on a pole and her head is impaled on a broken pipe, killing her instantly. William finds the cornfield Eli has planted and realizes that with its seemingly-perfect nature invulnerable to disease, able to grow out-of-season and in the worst of soil, it could be a highly-marketable product. Despite his wife's death, which Eli arranged, William finds backers and looks forward to the massive profits Eli's strain of corn will bring.
Eli neglects to inform his foster father of another property the corn possesses: it turns children who eat it into followers of "He Who Walks Behind the Rows." Eli decisively sways his high-school classmates towards his beliefs, turning them against the principal and directing them to abandon basketball and other previously-typical activities. Alarmed at Eli's converting the students, the principal attempts to inform other staff, but they don't believe him, as Eli's efforts have actually restored order at the school to a degree few had thought possible.
By the time Joshua realizes the full truth, Eli has killed their foster parents, the school principal, and Malcolm and Maria's parents, and he now has full control of his fellow students. Joshua confronts him, revealing that he has gone back to Gatlin (which resulted in Malcolm's death) and found the Bible of "He Who Walks Behind the Rows" which Eli holds sacred and, together with his own body, can survive indefinitely if one is intact. Eli roars "Give me the book!" and charges. Joshua throws it down, and as Eli scrambles to pick it up Joshua stabs Eli and the book with a sickle, destroying both.
After Eli dies, "He Who Walks Behind the Rows" rises from the cornfield: a grotesque monster with several tentacles. It kills several of Eli's followers who have slipped from his control in horrific ways, including T-Loc. After a brief struggle, Joshua repeatedly stabs the sickle at the monster's lower body, which resembles a large tree root sticking out of the ground. "He Who Walks Behind the Rows" collapses and dies.
As the film closes, the first shipment of Eli's corn arrives in Germany, the beginning of shipments all over the world.
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