WICKED, the organization charged with finding a cure to the disease called "The Flare", needs one last thing to complete their research - Thomas. Thomas is an escapee from WICKED who is determined to find out the truth about what WICKED is doing and how the world is slowly becoming destroyed from the virus called the Flare, a virus that changes a human into a snarling, crazed and cannibalistic monster.
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The story begins with Thomas being left by himself in a room for weeks without human interaction. One day, the "Rat Man" called Jansen, a lead scientist in the WICKED research, appears and tells Thomas he is extremely important. He tells Thomas that he has the Flare but he is one of the very rare who are immune to it. He tells Thomas that soon he will know the truth about WICKED. Thomas is reunited with his friends from the Glade (what they call the Maze that they were put in for their first experiment) and the other WICKED programs, including Theresa, Minho and Newt. Because she betrayed him, Thomas doesn't trust Theresa anymore. Jansen tells them all that they will be able to get their memories back via a surgery that will remove the chip in their brains that the scientists have been using to control and monitor them. Jansen also tells them there are a few among them who aren't immune to the Flare - including Thomas's friend, Newt. Jansen lets them decide if they want to go through with the memory-restoring surgery or not. Thomas, Minho and Newt all agree that they don't trust WICKED and don't want to do the surgery. Most of the rest of the kids decide to do the surgery, however.
Even though Thomas, Minho and Newt refuse the surgery, Jansen decides not to force them to do it anyway. In the surgery room, Thomas sees a friend, Brenda, who works for WICKED. Brenda helps Thomas and his gang to overpower the WICKED surgeons and guards. Together the gang try to escape WICKED. There is a commotion in the halls that attracts most of the guards so it is relatively easy for Thomas and his gang to make their way to the hanger. They are puzzled because they can't find any of the others. Eventually, they find out that the others have tied up most of the guards and escaped in a Berg (a sort of futuristic airship). Newt, becoming depressed that he is not immune and may succumb to the Flare, gives Thomas an envelope, making Thomas promise not to open it until the right time. They find another friend, Jorge, who, like Brenda works for WICKED but doesn't like what WICKED is doing. After an altercation with some guards, the gang escape on a Berg themselves.
They fly to Denver, which is a city where the Flare has apparently been kept out. It is Brenda's idea to go to Denver because she thinks Thomas, Minho and Newt may still be under the control and observation of WICKED because of the chips in their brains. She knows of an ex-WICKED doctor who can help remove/deactivate the chip. In Denver, Thomas is approached and given a message by a stranger - a message from an old enemy from his time in the Glades, Gally. Gally had killed a good friend of Thomas and Thomas had beat Gally into a pulp. Thomas thought Gally was dead. They find Gally and Gally explains that after Thomas beat him up, he was taken back to the labs where he pretended to have become insane so that WICKED would let him go. There he joined an organization called The Right Arm, which is an organization set on toppling WICKED. Gally asks Thomas and his gang to join him. Thomas tells him he'll think about it.
Later on, Thomas and his gang find the ex-WICKED doctor. Thomas' fail safe program is activated, causing him to lose power over his own body. He resists with all his might, nearly killing the doctor. In the end, he is subdued and the surgery proceeds successfully. As the gang hang out in a coffee shop while deciding what to do next, they find themselves in the middle of a bust. The cops/Red Shirts who are in charge or scanning everyone to ensure they are virus-free find a person who has the virus and take the person into custody. Because Thomas acts suspicious and reveals he is a "Munie" (a person immune to the Flare), the Red Shirt kidnaps Thomas because he is worth a lot. Later on, the Red Shirt is killed by a WICKED cop machine. On the screen of the cop machine, Jansen again tries to convince Thomas to rejoin the WICKED program. To get Jansen to leave him alone, Thomas agrees to think about it. Before he leaves, Jansen tells Thomas that Newt is succumbing very quickly to the Flare.
Thomas reunites with his gang and relays the news about Newt. Together, they make their way back to the Berg where they find that Newt is gone. Newt left a note saying that he was taken by bounty hunters and he's gone to join the other "Cranks" (people who have turned insane from the Flare). Brenda knows that they keep the people succumbing to the Flare in a place called Crank Palace. The group fly over to the refugee camp where they meet some guards. They pay the guards to help them locate Newt. When they find Newt, however, he is angry and tells them to leave him alone. He almost shoots Thomas to make his point. He tells Thomas that the Cranks are planning to storm Denver. Thomas and his gang are shaken by the change that has come over Newt. They barely make it out of Crank Palace alive. Thomas opens the envelope and reads the letter that Newt left form him. In it, Newt asks Thomas to kill him if he is his friend.
When the gang return to Denver, they are immediately taken hostage by some bounty hunters who dump them in a room full of other Munies including Theresa. The gang find out that the Right Arm is responsible for their kidnapping. Thomas is confused as he thought the Right Arm were on the same side as him so he demands that the bounty hunters take him to their leader. After a harrowing ride to the headquarters of the Right Arm, Thomas and Brenda meet with Gally who introduces them to the leader of the Right Arm, Vince. Thomas convinces Vince that he can be useful to the Right Arm because WICKED wants him as the Final Candidate for their research. Vince explains that they aren't actually kidnapping the munies - they are simply imitating what WICKED is doing so that they can blend in with the WICKED operations. WICKED is apparently recruiting more munies to do a fresh round of research. Vince reveals that the purpose of the Right Arm is to topple WICKED because they believe that there is no point to unjustly killing innocent children for the sake of a non-existent cure when the world should be focused on preserving what few survivors they have left. Vince asks Thomas to plant a jamming device inside WICKED that will disable their weapons and allow the Right Arm to have a fair chance at overcoming WICKED. Thomas agrees to help them in their plan. On their way back to the place where the other munies are, Thomas runs into Newt. Thomas kills Newt to stop his friend's suffering.
The Right Arm drop off Thomas near WICKED where he gives himself up to Jansen. Thomas finds a way to set off the jamming device in a bathroom. He learns that the final test Jansen needs from Thomas is his brain. That his brain will save the world and he will have made the ultimate sacrifice for humanity. They allow Thomas time for the idea to sink in. Thomas is torn between truly wanting to help everyone find a cure and not wanting to die. Eventually, he gives in and he is prepped for the surgery. During the surgery, the Right Arm launch their attack. When Thomas wakes up after blacking out, he finds a letter from Chancellor Paige, one of the heads of the WICKED program. The letter says that she disagrees with what WICKED is doing and that Thomas should get himself out of WICKED and save the other munies. Chancellor Paige also leaves behind a map with directions to where to find the munies and how to escape through the Trans, which is a sort of portal.
Thomas realizes that the munies are held in the Maze. He finds them in the Maze and organizes their escape. Thanks to the Right Arm planting bombs all over WICKED, the entire roof of the Maze is collapsing - the bombs have already dislodged chunks of roofs that have killed some of the munies. Thomas and his gang lead the munies out of the Maze and through the Trans where they are transported away from WICKED to start their life anew.
Best part of story, including ending:
I like how fast-paced the story was - it was an endless string of action. At the same time, I feel like the story could benefit from more explanations to the many questions posed from the other books int he series.
Best scene in story:
My favorite scene was when Thomas finds his way back to the Maze - it's a feeling of dread but also a nice full circle for the series.
Opinion about the main character:
I like the rapport Thomas has with his most loyal friends, Minho and Newt.