Isolation. That is all Thomas can think about for 2 weeks. After Wicked, an organization that locked Thomas inside the room, lets him free, Thomas goes and sees his friends, Newt and Minho and Teresa. Thomas and his friends receive some important news after their reunion. They will get their memory back, which Wicked stole from them.
I can't believe we're back here
They learn something else. Newt is not immune to the deadly virus called the Flare. He will die in a few weeks. When it's time to get their memories back, Thomas, Newt, and Minho escape, thinking it's a trap, and meet two old friends who helped them live in the desert, Brenda and Jorge. Brenda stays and fights with them while Jorge prepares the aircraft to escape.
I only ever...cared for...
After they land at a city, some officials find Newt and take him away to a Crank camp. Cranks are people infested with the Flare. On their way to save him, they met Gally, their old friend, who is part of the Right Arm. Lawrence, another member of the Right Arm, helps them get to the Crank camp. Newt would not leave and he tells Thomas to kill him. So Thomas does.
These sunsets are so beautiful.
Thomas finds Teresa, and the five teenagers are reunited. Thomas learns form the Right Arm that Wicked will put all the remaining immune people through a cruel test called the Maze. Since the five friends know what pain the Maze brought to them, they decided to rescue the immunes. So they travel back to the Maze for the second time.
While they were in the Maze, The Right Arm arrived at Wicked's headquarters and started blowing things up. To make things worse, monsters called Grievers started attacking and killing the people. As a rock was about to fall on Thomas, Teresa pushed Thomas and the rock fell on her.
The head of Wicked, Janson, makes on last attempt to stop them, but after a brutal battle, Thomas kills him. Then they walk through a teleporter that brings them to this paradise. To make sure that no one will follow them, Brenda sets fire and destroys the teleporter. There, the remaining people will start a new life, with no virus to end them all.