Thirteen-year-old Twig, having always looked and felt different from his woodtroll family, learns that he is adopted and travels out of his Deepwoods home to find the place where he belongs.

In his continuing adventures, Twig, now sixteen years old, joins the crew of his father's sky pirate ship and embarks on a dangerous mission to collect the powerful stromphrax, a substance that purifies water and also prevents the city of Sanctaphrax from floating away.

Rook Barkwater, one of the apprentices chosen to make a dangerous journey to study in the Deepwoods, joins the sky pirate Captain Twig in opposing the Guardians of the Night and learns more about his own past.

Fleeing from the ruins of New Undertown, Rook Barkwater and the librarian knights and Felix Lodd and his banderbear friends must lead the escaping population to a new life in the Free Glades.

Quint finally begins his training at the Knights Academy, Maris adjusts to life in Undertown, and Sanctaphrax shivers in anticipation of a legendary storm, while a storm of a different kind brews between sky-scholars and earth-scholars.

Cade Quarter is building a new life for himself in the wild of the Farrow Ridges, miles away from civilization - and from the enemies who are seeking him. But when his new home is threatened by villainous mire-pearlers, Cade and his friends must find a way to defend the land they love.