A young boy, Thomas, is taken in by Ava Paige (Patricia Clarkson) and troops from the organization WICKED, alongside other children, after being dropped off by his mother for his own safety. Years later, shortly after the remaining Gladers escaped The Maze, the Gladers - the now teenage Thomas (Dylan O'Brien) and Teresa Agnes (Kaya Scodelario), former workers of WICKED and creators of the Maze, Newt (Thomas Brodie-Sangster), Minho (Ki Hong Lee), Frypan (Dexter Darden) and Winston (Alexander Flores) - are taken to a facility run by Mr. Janson (Aidan Gillen). He explains that the facility is a safe haven for Immunes of the Flare virus, protecting them from WICKED and the Cranks, and providing them clothes, food, and sanitation, where survivors of other mazes are also present. Thomas becomes curious about their activities and manages to find out what is really happening behind the closed doors. With help from Aris Jones (Jacob Lofland), the first maze survivor to end up in the facility, it is revealed that WICKED's leader, Ava, is still alive and that Mr. Janson is working for them as the two discuss the lethal experiments being conducted on the Immunes and that Janson has yet to find The Right Arm, a resistance group located in the mountains. The group, including Aris, escapes the facility as Janson orders his WICKED troops to track them down and they find themselves in the deserted outside world - the Scorch
Thomas and his fellow Gladers face their greatest challenge yet: searching for clues about the mysterious and powerful organization known as WCKD. Their journey takes them to the Scorch, a desolate landscape filled with unimaginable obstacles. Teaming up with resistance fighters, the Gladers take on WCKD’s vastly superior forces and uncover its shocking plans for them all.