Gregor and the Marks of Secret is the fourth book in the Underland Chronicles, published in the U.S. by Scholastic Press on May 1, 2006. While his mother goes through recovery, Gregor visits the Underland more and more often. During his training with Ripred, the rat tells him that it is time that they kill the Bane.

Uneasy about his new task, Gregor shows up to his next session, only to find Ripred has turned up missing.

Over the next few days, Gregor is invited to Hazard's 7th birthday party, where he takes pictures of the event and teaches children songs from the Overland.

During a dance with Luxa, Gregor begins to realize his feelings for her, before they are interrupted by a golden crown falling between them. Luxa realizes her friends, the Nibblers, are in danger, and sets off with Gregor, their bonds, Howard, Nike, Boots, Hazard, and a young bat named Thalia.

On their journey, they discover the Nibblers are in peril, and that the Bane has created a plan to get rid of them for good.

A war is started, the Underland is threatened to be destroyed, and Gregor faces a new prophecy that may change his world forever.