Thomas, Newt, and Frypan are the last of the free “Gladers” immune to the Flare virus that has ravaged the world’s population. Against the orders of Vince, who now leads The Right Arm resistance, the three leave their camp to rescue their immune friend Minho, who is being tortured by the organization WCKD in hopes of developing a cure for the virus. Heading for the “Last City”, where WCKD’s headquarters is located, the group is attacked by Cranks, humans infected with the Flare. However, they are saved by Jorge and Brenda, who join them.
The group makes it to the wall of the Last City, which protects the city from Cranks. Outside the wall, people are rallying in protest to be let into the city. When WCKD opens fire at the protesters, the group is captured by a contingent of masked men and are taken to a hideout. One of the masked men is revealed to be Gally, who has survived Minho’s attack at the end of The Maze Runner. Gally takes them to see Lawrence, a rebellion leader for those outside the walls, who grants them permission to enter the Last City through a secret entrance. Gally leads Thomas and Newt through to the city and, spotting Teresa, Gally tells Thomas that she can get them into WCKD headquarters. The three capture her and she agrees to help them.
Thomas, Newt, and Gally escort Teresa inside WCKD headquarters and toward the location of the Immunes. Gally looks after the Immune children and stays to find a serum that can treat the Flare, while Thomas, Newt, and Teresa go to find Minho. They are caught and chased by a vengeful Janson, who leads WCKD’s troops. Teresa lets them escape to find Minho, before rushing to do a blood test on Thomas’ blood, which she obtained when removing trackers from the Gladers.