| Spoiler Alert!|
This page contains details about the plot which may lower your enjoyment of the books and/or movies. Discretion is advised.
- The main premise of the book is that the Gladers are forced by WICKED to participate in a second Trial, having to complete the task of reaching the other side of the Scorch. The main premise of the movie, however, is that the Gladers actually escape from WCKD and their experiments and end up out in the Scorch. As such, the titular trial is absent in the film, which as a whole is a very loose adaptation of the book.
- Following their escape from the Maze, the Gladers are not taken to a three-room building to recover from the maze, and prepare for the next assignment. Instead, they are taken to a rather large facility, where WCKD intends to perform experiments on them.
- The group traversing the Scorch in the film is much smaller, and consists of most named characters of the book.
- Unlike the book, Winston does not die in the thunderstorm, but instead is bitten by a Crank. He commits suicide before he can turn fully zombie-like.
- Also unlike the book, Teresa is not separated from the other Gladers long-term. She is briefly taken by WCKD, and rescued by the Gladers before escaping to the Scorch with them.
- There is no mention of different stages of the Flare. All victims encountered behave zombie-like.
- It appears in the film, WCKD puts the Maze Trial experiments in a coma, draining a blue liquid serum from them. This is what Aris shows Thomas before they realize that they need to escape before they are taken there. In the book series, WCKD uses the test subjects' brain patterns to try to analyze a blueprint for the cure.
- It is shown in the film that you have to be bitten by a "Crank" in order to receive the deadly virus, unlike the book where the virus is merely airborne.
- In the beginning of the film. Teresa is taken off seperately and given her memories back. However, this did not happen until The Death Cure.
- The The Right Arm and Vince do not make an appearance, nor are they mentioned until the The Death Cure, but both appear in the second movie. The Gladers overhear WCKD discussing the Right Arm, and cross the Scorch because they hope they will find shelter with them.
- Additionally, a character working for the Right Arm named Mary was created specifically for the movie franchise.
- In the movie, Jorge and Brenda are explicitly said to not have the Flare when they are encountered, and run a camp of survivors rather than a camp of Flare-victims. Their motivation for following the Gladers across the Scorch is that they also hope to find security from the Right Arm.
- In the novel, Brenda is immune and working for WCKD at first, but this is not the case in the Maze Runner Film Series. She is bitten and infected, but Thomas' blood/serum cures her as proven in the Death Cure film.
- Thomas is never shot in the shoulder in the film.
- Sonya and Harriet are not working with Teresa, but for the Right Arm instead.
- In the movie, Teresa betrays Thomas and the Gladers by giving away their location to WCKD, rather than luring only Thomas into a gas-chamber as she did in the book. Aris has no part in the betrayal.
- The book concludes with the Gladers completing their task and getting rescued by WCKD. Thomas is separated from his friends and locked in a small white room beginning the third phase of the WCKD's trials. The movie ends with the Gladers and the Right Arm receiving a crushing defeat from WCKD, during which Minho is recaptured. The Gladers swear to free their friend from his imprisonment. The book ends very differently. Thomas, Teresa, Minho, Newt, and the other test subjects along with Brenda and Jorge end up completing WCKD's second trial in which they were promised a cure in the end. WCKD takes them all back to main headquarters. In the end of the book, Thomas is separated from the group in a white room.
- In the book, there were only two groups: Group A and Group B. In the movie, there are more than two groups. It is unknown how many groups there are, as it was never mentioned. Since Groups A and B had a particular ratio for gender (Group A having all boys and one girl, Group B having all girls and one boy), it can be assumed that some of the extra groups were mixed.