Thomas, Newt, and Frypan are the last “Gladers” immune to the Flare virus that affected the entire human population. They attack the WKCD train to save their colleague Minho. But they are failing the wagon and Minho is transported to the “Last City,” the WKCD operations base. In spite of orders from Vince’s The Right Arm, the three leave their camp to enter the city and recover Minho.
The group manages to sneak through a tunnel, but they are attacked by the Cranks, some people foolish by Flare. They are saved by Jorge and Brenda who have followed them secretly. In the WCKD headquarters, where the virus begins to spread by air, the serum created from Minho’s blood is tested on a girl infected with the Flare virus and seems to work at first but ultimately fails to Teresa’s frustration now works with WCKD to develop a cure after betraying Thomas and the rest of the group.
The group reaches the edge of the Last City wall that surrounds and protects the city from zombies. Outside the wall, the group goes among virus-infected people protesting to be left in the city. But patrol troops of the WCKD open the fire on the protesters to remove them. In the chaos that occurs, Thomas, Newt, Frypan, Brenda and Jorge are captured by a group of masked men and taken to their hiding place where one of them turns out to be Gally, who survived the wounds produced by Minho.