Maze Runner: The Scorch Trials picks up immediately after the events of the first film. Thomas and his fellow Gladers—Newt, Minho, Frypan, Winston, and Teresa—believe they have escaped the dangers of the Maze when they are taken to a facility run by the mysterious organization WCKD. There, they meet other survivors from similar mazes. At first, the place appears safe, offering food, shelter, and protection. However, Thomas soon realizes that WCKD has sinister motives, experimenting on the immune youth to find a cure for the deadly Flare virus.

With the help of a boy named Aris, Thomas discovers that the facility is another trap. He convinces his friends to escape, and together they flee into the outside world—known as the Scorch. This desolate wasteland is filled with crumbling cities, brutal sandstorms, and infected humans called Cranks. As they trek across the dangerous landscape, the Gladers face devastating losses and life-threatening encounters that test their strength and loyalty.
Along the way, they encounter resistance fighters known as the Right Arm, who are waging war against WCKD. Thomas hopes to find safety with them, but their journey is complicated by betrayals and shifting alliances. Most devastating is Teresa’s choice to side with WCKD, believing their methods may save humanity.
In the climactic confrontation, WCKD strikes against the Right Arm, capturing Minho and others. Thomas vows to rescue his friend and continue the fight against WCKD, setting the stage for the final battle.
The film expands the world of The Maze Runner, shifting from the confined setting of the Maze to a vast, apocalyptic environment. It emphasizes survival, trust, and the moral dilemmas of sacrificing individuals for the greater good, while delivering intense action and suspense.