Thomas has been running around ragged during the first two books of The Maze Runner series: first he had to escape the Maze with his Glader friends in Book One; then, in Book Two, he had to endure the Scorch Trials, a deadly trek through a hot, barren wasteland. Talk about having a bad few weeks.
Well, at the end of Book Two, we left Thomas in a white room, alone. He just completed the Scorch Trials, and word has it that he has the Flare, so WICKED has him quarantined. Ah, what a life it is.
We pick up where we left off: Thomas is in that same white room. He has to stay in isolation for 26 days before they finally open the door. We'll give it to you straight: Thomas ain't so happy with WICKED. Yeah, well, happy or not, they let him out, and Rat Man, the dude who gave Thomas his orders for the Scorch Trials, escorts him into a room full of his Glader pals. So everyone is back together.
Almost immediately, Rat Man tells everyone that they'll be given their memories back. Most people are pumped about this, but Thomas, Minho, and Newt aren't buying anything WICKED says. Plus, Rat Man also lets everyone know who is immune to the Flare and who isn't. Most people are immune, but Newt isn't, which is a total bummer. He's got the Flare.
Naturally, Thomas, Minho, and Newt rebel against having the surgery. At first they succeed in their rebellion, but eventually they're foiled and put in separate rooms.
In Thomas's operating room, we find Brenda—you know, the girl he saw out in the Scorch who helped him get to safety. It turns out that Brenda actually works for WICKED. But it's all good—she doesn't like WICKED at all, and she helps Thomas escape the memory surgery. Thomas and Brenda then break Minho and Newt out, and after a bunch of action-packed sequences, the four reach the hangar, where Jorge (the dude from the Scorch) is ready for them.
More action: kaboom, kaplow. Our heroes all make it safely to a Berg (an airship thing), and they fly to Denver, where the other Gladers (Teresa and all of those other people) supposedly flew to as well. When they arrive in Denver, Newt has to stay on the plane because he's starting to feel the effects of the Flare.
Thomas immediately receives a note from Gally, the boy who killed Chuck back in Book One, telling Thomas to come meet him. Brenda wants them all to go meet a dude named Hans because he's a doctor who can remove chips from the boys' brains (these are the chips that let WICKED track them). But Thomas decides that they should meet Gally first.
The gang (Thomas, Minho, Brenda, and Jorge) meets up with Gally, who reveals that he's part of an underground group called the Right Arm. These people hate WICKED (well, well—so does the gang), and they need Thomas's help. Thomas agrees, but first they need to get to Hans so they can stop being tracked by WICKED.
The gang goes to Hans, and he agrees to take Thomas's and Minho's chips out. But WICKED starts controlling Thomas right before the procedure, leading to a wacky scene in which everyone's trying to restrain Thomas. Don't worry: they sedate him, and Hans takes out everyone's chips. Phew.
The next morning, our heroes plan to meet up with Gally, but Thomas gets caught up in an altercation between a government official and a man who's on the Bliss drug. This leads to Thomas being held hostage by the government official, who's really just another kind of bounty hunter. Luckily, the bounty hunter is shot by a machine controlled by WICKED. Then Rat Man Janson gives Thomas an ultimatum: Thomas needs to go back to WICKED to help them finish the blueprints. If not, WICKED will never find the cure. Also: Newt is in big trouble.
Thomas decides the second part of this message is much more important than the first, so the gang rushes back to the Berg. They find a note inside telling them that Newt was brought to a place with other Cranks called Crank Palace.
And off the gang goes to Crank Palace.
In Crank Palace, our heroes find Newt, but he isn't happy to see them. In fact, he tells them to leave and threatens to shoot them with a Launcher. Newt had been rapidly losing his sanity, and at this point, he's pretty out of it. The gang is forced to leave Newt, which breaks the hearts of Thomas and Minho.
When they reach their Berg again, our heroes are again arrested by some random people with weapons. Eventually, they're thrown into a room filled with people, but not just any people: they're totally reunited with some other Gladers, including Teresa. After Minho and Thomas start a quick mutiny against their captors, they're able to figure out that their captors are part of the Right Arm—which is odd, because they're supposedly the good guys.
Thomas convinces one member to drive him and Brenda to the Right Arm's boss. When Thomas meets the boss, Vince, he's told that the Right Arm needs Thomas to infiltrate WICKED's headquarters. Oh, yeah: it's battle time.
But first, it's time to break out the tissues. On the van ride to the hangar, Thomas sees Newt hanging around on the highway. Thomas gets out of his van and tries to tell Newt to come with them, but Newt attacks Thomas. Newt keeps screaming at Thomas to kill him. After a lot of screaming and struggling, Thomas puts Newt out of his misery.
Now that Newt's dead, Thomas is absolutely distraught and makes his way to WICKED's headquarters with the help of the Right Arm and their Berg. When he enters WICKED's headquarters (alone), he's told that he's the Final Candidate and that WICKED needs his brain. That's right: they need Thomas to be a sacrifice so that they can save mankind.
Pshh. Yeah, right.
Thomas goes to the bathroom and plants a device that helps the Right Arm disable WICKED's weapons. Then he stalls for a while.
Yeah, well, he can't stall forever, and he's eventually brought to the operating room.
The Right Arm starts infiltrating the headquarters while Thomas is about to be operated on, and this forces the physicians to try to get the procedure done quickly. Thomas is sedated, but when he wakes up, he finds a note from Chancellor Paige. It says that she stopped the procedure and that Thomas needs to free the rest of the immune people WICKED had gathered and head to a Flat Trans, which will then lead them to a new life. Seeing that this is Thomas's only chance, he follows Paige's orders.
Thomas does exactly what the letter says: he meets up with the rest of his gang, and then they go back into the Maze, where they find 200 or so immune people. Just as they make their way back out of the Maze, the whole Maze starts blowing up: the Right Arm was apparently planning on destroying the whole headquarters. Tons of people are crushed by falling ceiling stones, but our heroes eventually make it to the exit room, where the Griever pods are.
Just as they're about to leave, Grievers start coming to life. Thomas kills all of them but one, and the last one slices a few people to pieces. Luckily, Thomas is able to kill that one, too—right before it slices through him. Our heroes exit the Maze, and they rush towards the Flat Trans. It's soooooo close.
But not close enough. As people start hopping through the Trans, Janson and his guards attack Thomas and his friends. Of course, Janson has no chance, and Thomas ends up strangling the dude to death. Ah, sweet revenge. Finally, Janson's dead, but another ceiling tile starts to fall onto Thomas. Teresa pushes him out of the way, but she's squished. Teresa: dead.
Oh, well, time to move on. Everyone goes through the Flat Trans, and on the other side is a paradise. Like, a legit paradise with green everywhere and an ocean and everything. Thomas has finally made it, and the book ends with him and Brenda kissing. Teresa who?
But that's not really the end. See, we get another epilogue with a memorandum from Chancellor Paige. In her memorandum, she says that the paradise for Thomas and the 200 or so Immunes was WICKED's Plan B. Once their Plan A had been ruined, they decided the only way to save the human race was to get a bunch of immune people to start civilization all over again; to do this, she made Brenda and Jorge help Thomas make it to paradise.
In the end, WICKED does end up saving the human race, despite the awful crimes they've committed against humanity.