Thomas, Newt, and Frypan are the last of the free "Gladers" immune to the Flare virus that has ravaged the world's population. They and The Right Arm resistance conduct a rescue operation where they retrieve other Immunes from a train operated by WCKD, an organization responsible for capturing and experimenting on immune children. They discover that Minho, their remaining Glader friend whom WCKD had captured, was not on that train, which is headed to "The Last City", WCKD's base of operations. Against the orders of Vince, leader of The Right Arm, the three leave their camp to rescue Minho, who is being tortured by WCKD in hopes of developing a cure for the virus. Heading for the Last City, the group is attacked by Cranks, humans infected with the Flare. However, they are saved by Jorge and Brenda, who join them.