In the midst of war, Eglantine unwittingly becomes a spy for Kludd, leader of the Pure Ones (a group of evil owls). She is brainwashed by an owl sent by the Pure Ones to infiltrate the Great Ga’Hoole Tree. Her odd behavior eventually attracts attention, and Soren and his friends vow to find out what's wrong with Eglantine. They ultimately learn what happened and help her reverse the effects of the brainwashing. Kludd continues to battle against the Guardians of Ga’Hoole for control of their tree. In the end, Kludd and his forces are defeated. But his conflict with Soren is not yet over.

Soren's beloved mentor, Ezylryb, is finally back at the Great Ga’Hoole Tree. But all is not well. There's a war between good and evil in the owl kingdom. On one side is a group led by Soren's fearsome brother, Kludd, who wears a terrifying metal mask to cover his battle-scarred face. On the other side are the owls of the Great Ga’Hoole Tree, who must fight to protect their legendary tree from Kludd's attacks.

Now that Soren has been reunited with this sister, Eglantine, he must face his new challenge: making sense of the mysterious disappearance of his mentor, Ezylryb. When Soren discovers that Ezylryb is in danger, he and his friends Gylfie, Twilight, and Digger devise a plan to save their teacher. In this process, Soren fights a ferocious foe who wears a terrifying metal beak, sharpened for battle. It's not until the confrontation is over that Soren discovers the true identity of his opponent...