Gregor and his toddler sister, Boots, fall through a grate in their laundry room and land in the Underland, a world far beneath the earth's surface populated by humans, as well as giant intelligent bats, rats, cockroaches, and spiders. Taken in by the humans who live in an underground city, at first they only want to find a way back home. But then Gregor learns that his father, who disappeared years before, is in the Underland too, held prisoner by the rats, who are about to launch a war on the humans.
The humans are allied with the bats, and the spiders and roaches are in the middle. But an ancient prophecy talks about the coming of a warrior from the Overland to unite them to defeat the rats, and the Underlanders think that Gregor is the warrior of the prophecy.