Plot

A young boy, Thomas, is 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 the remaining Gladers escaped The Maze, the Gladers - the now teenage Thomas (Dylan O'Brien) and Teresa Agnes (Kaya Scodelario), former workers of WCKD 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 WCKD 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 WCKD'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. Ava orders Janson to start harvesting all the remaining Immunes, & Janson suggests that they get started with the latest batch of arrivals (Thomas's group).

The group, including Aris, escapes the facility as Janson orders his WCKD troops to track them down and they find themselves in the deserted outside world - the Scorch. The group arrive at an abandoned marketplace, where they first encounter the Cranks, humans Zombified by the Flare. In the process, Winston gets infected by one of them. When morning comes, they find the city has turned into ruins and that WCKD is still searching for them. Winston's infection gets worse, forcing the rest of the group to leave him alone to die by shooting himself, preventing his transformation.

The group continues to venture the desert until one night; while sleeping in the middle of the desert, Thomas wakes to discover civilization on the distant horizon. As a thunderstorm emerges, they run to an abandoned facility for shelter. To the group's relief, Minho survives being struck by a bolt of lightning. They manage to enter the facility, only to find that it is filled with chained Cranks.

The group meets Brenda (Rosa Salazar) and Jorge (Giancarlo Esposito), who lead a dangerous band of survivors and have used the Cranks as their own guard dogs. When the two find that the group had come from WCKD and is looking for the Right Arm, the two agree to take them to the Right Arm, abandoning their group of survivors. Moments later, WCKD, led by Janson, storms the place, only for the facility to be destroyed by Jorge's explosives, however, Thomas and Brenda are left behind as the rest have escaped with Jorge. Thomas and Brenda manage to escape the Cranks, only for Brenda to get infected by a Crank in the process.

Thomas experiences a flashback of when he and Teresa were working for WCKD, in which Thomas tries to warn Teresa of WCKD's plans, only for the two to be separated by WCKD's troops. As Thomas and Brenda reunite with the rest of the group, Jorge interrogates Marcus (Alan Tudyk), a survivor who secretly works for WCKD, into revealing the whereabouts of The Right Arm. The group eventually arrive at The Right Arm's relief camps, where other innocent survivors are present, and are greeted by Vince (Barry Pepper) who leads the Right Arm and is in charge of deciding whether they can stay or not. As Brenda's infection gets worse, Vince threatens to shoot her, only to be stopped by Mary Cooper (Lili Taylor), a former WCKD scientist who reveals that Thomas was their informant.

As Mary halts Brenda's infection using an enzyme cure, Mary explains that the enzyme can only be harvested from an Immune's body, not manufactured, and that arguments over the methods of manufacturing the cure with Ava led to Mary's departure from WCKD. That evening, Teresa informs WCKD of her location, believing their motivations are good, leading to an ambush by the organization. Ava and Janson arrive and confront the Right Arm before WCKD troops capture survivors for experimentation, including Minho, while Janson shoots Mary dead. After Thomas and the Right Arm fend the WCKD troops off, Ava, Janson, and Teresa retreat with their captured survivors.

With only a fraction of survivors left at the site, Thomas plans an infiltration into WCKD and is determined to take them down to save his friends and civilization, with Vince and the Right Arm agreeing to help and prepare to fight back.