A community of quirky, mischievous creatures who have lovingly raised an orphaned human boy named Eggs in the amazing cavernous home they've built beneath the streets of Cheesebridge. When the town's villain, Archibald Snatcher, comes up with a plot to get rid of the Boxtrolls, Eggs decides to venture above ground, 'into the light,' where he meets and teams up with fabulously feisty Winnie. Together, they devise a daring plan to save Eggs' family....

The outer crust is under attack by the subterranean Styx who are turning ordinary humans into walking bombs and incubators for their eggs, and only Will Burrows and his band of retired commandos stand in their way--but the Styx also have problems of their own.