The film begins with a young boy, Thomas, taken in by Ava Paige (Patricia Clarkson) and troops from the organization WCKD, alongside other children, after being dropped off by his mother for his own safety. Years later, shortly after being rescued from the maze, Thomas (Dylan O’Brien) and the remaining Gladers – Newt (Thomas Brodie-Sangster), Minho (Ki Hong Lee), Teresa Agnes (Kaya Scodelario), 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, protecting them from WCKD, the Flare virus and the Cranks, and provides them clothes, food, and sanitation, where there are other survivors of multiple 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 WCKD’s leader, Ava, is still alive and that Mr. Janson is working for WCKD, as they discuss about the experiment on the Immunes and that Janson has yet to find The Right Arm, a resistance group located at the mountains. The group, including Aris, escapes the facility, as Janson orders his WCKD troops to track them down, where they find themselves in the deserted outside world – the Scorch.