Following their harrowing escape from the Maze, Thomas and his fellow Gladers are brought to a remote facility run by Mr. Janson, who claims to be their rescuer, part of an organization that combats the catastrophic viral outbreak known as the Flare. The survivors are introduced to other groups of teens that have been 'rescued' from different mazes, and they begin to acclimate to a semblance of safety in this guarded haven. The group, including Teresa, Newt, Minho, and others, slowly start to question their circumstances as strange observations unsettle them. Thomas, in particular, grows increasingly wary of their protectors, driven by instinctive mistrust and cryptic messages from a familiar figure presumed dead.

Doubts turn into fears as Thomas and a few Glade survivors make a shocking discovery that reveals the true intentions of their supposed saviors. The group decides they must escape the facility and embark on a perilous journey across the desolate landscape known as the Scorch. The Scorch is a wasteland filled with a myriad of dangers including relentless heat, unpredictable storms, and hideously transformed survivors of the Flare infection. Their quest brings them in contact with resistance fighters, leading to a deeper understanding of the world they've found themselves in and hinting toward a larger, ongoing battle against the sinister forces at play.