Thomas, Newt, Frypan, Minho, and all the others that made it our of the maze are stuck in a building with the leaders dead, Teresa missing, and a weird man behind invisible glass that has told them that they are to walk through a flat trans in the morning at exactly 6:00 a.m. Cranks are outside trying to get inside the building.
As the Gladers and Aris walked through the flat trans, they entered a pitch black tunnel. As they walked down the tunnel, they heard a low voice that kept telling them to turn around and go back. When they were about a mile into the tunnel, a boy fell and his head was eaten off by a large, hot, and solid metal ball. At the end of the tunnel, they stepped into blinding light and another boy was attacked by a metal ball and survived. They then stepped into the Scorch.
As the Gladers were walking in the scorch, they gain ground on the city. Before they reach the city, a large multitude of black clouds cover the sky. They thought rain was coming, but lightning rained from the sky in waves. Many Gladers died from being struck by lightning. Minho was was struck and fell. Thomas picked him up with Newt and kept going. They made it to the closest building in the city and layed down. Rain poured after they made it to the building.
In the underground tunnels of the city, Brenda and Thomas are running from the Cranks that are way past gone. They hide in a hole inside a room and wait for the Cranks to pass. When they think the Cranks are gone, they come out of the hole. Thomas is grabbed at the neck and pulled out of the hole. Brenda stabs the Crank in the arm and comes out of the hole to help Thomas. The Crank grabs Thomas again but Brenda holds the Crank by the arms. Thomas has the choice to stab the Crank and he hesitates. Eventually, Thomas stabs him.
Teresa and Group B, including Aris kidnap Thomas and bring him to the mountains. Teresa plans on killing Thomas with Aris. Teresa and Aris throw Thomas into a dark room after a strong fight with Thomas. Thomas gets knocked out by gas. WHen he comes out, Teresa and Aris are waiting for him and they walk down the mountain and out into the desert towards Group B and the Gladers. Everyone fights large beasts with light bulbs.
After killing all of the beasts with the light bulbs, there are many people that are dead. Everyone gets into the Greaver eggs that the beasts came in and wait. The lightning storm comes again when they are fighting the beasts. Many more people die from being hit by lightning. A plane from WICKED comes to the battle scene and opens the hatch. As many people as possible board the plane. A man tells them that they have to pick either Jorge or Brenda. They pick both and threaten to kill the man. Everyone gets to take a shower, nap, and eat.