Basically, people called Creators put a bunch of boys whose memories were erased into a Maze in Book One of The Maze Runner series. Thomas, the protagonist, was one of the last ones to be put in the Maze, along with a girl named Teresa, the only girl, and that's when things got strange. Lots of shenanigans went down, but the boys eventually found out how to escape. Once they escaped, they were "rescued" by some sort of rebel group, and then they were brought to a safe haven where they could sleep, and stuff like that.
Got it? Good.
The Scorch Trials opens with the boys—we call them Gladers—all in their dormitories having a grand old confusing time, when a new something bad happens. Crazy people outside—they're called Cranks—start screaming, so the boys all race into Teresa's room to see if she's okay. On the way, they find a bunch of dead bodies hanging from the ceiling of the hallway. Great. Then, when the boys get to Teresa's room, they find that she's gone; a boy named Aris is in her room instead.
Okay, so things just got really weird.
No one knows what's going on, and when the boys get back to the hallway, it turns out that the dead bodies are all gone.
Later, a random dude just appears in the central room of the dormitories. He sits in a chair and reads a book, and he's also protected by a force field. Eventually, he breaks his silence and tells the boys what's going on. He's part of WICKED, and the scoop is that the boys are all about to be put into a trial. At 6 a.m., they'll need to go through a Flat Trans—whatever that is—and then enter the Scorch, where they'll need to reach the safe haven in exactly two weeks' time.
Sounds easy, right?
Actually, no. That doesn't sound easy at all.
Anyway, the next morning, the kids all go through the Flat Trans. It's a dark portal thingy, and bad stuff happens inside. A few kids get their heads sliced off from metal ball things, but eventually, most of them reach the other side. Phew? Meanwhile, Thomas tries telepathically to reach Teresa, but she isn't responding, which is pretty alarming.
When the boys exit the Flat Trans, they walk out into the Scorch, which is pretty much a barren wasteland with extreme heat. Up ahead is a city filled with Cranks, and ahead of the city is a mountain range. The boys need to make it past the mountain range.
The boys make their trek to the city, but a storm hits and blows a few of them to pieces. Things are going fantastically, as you can tell.
When the boys reach the city, they run into a Crank dude named Jorge, who claims he's the leader of the Cranks. He wants to kill Minho so much, but Thomas talks him out of it. In fact, Thomas talks Jorge into helping the kids, as their safe haven supposedly has the cure for the Flare, the disease that all of the Cranks have.
By the way, the kids all have the Flare, too—it just hasn't affected their brains yet.
Jorge starts to lead the boys toward the mountain with another Crank named Brenda, who's super smart. Unfortunately, Thomas and Brenda get separated from the rest during a Crank attack.
Brenda helps Thomas make his way through the city by taking him through an underground tunnel system. On the way, the pair is attacked by some crazy Cranks, but everything turns out okay. When Brenda and Thomas reach the center of the city, Thomas finds a sign that says he's the true leader. Apparently, these signs are everywhere, which is why Jorge and Brenda ended up helping him.
But Thomas and Brenda get in trouble pretty quickly: a group of Cranks force them to attend their party, where Thomas and Brenda are drugged and captured. Luckily, Minho and the Gladers ambush the party and save Thomas and Brenda.
Once again, Thomas has the worst luck: one of the Cranks turns out to have a pistol, and he shoots Thomas in the shoulder. To make things even weirder, WICKED sends a flying-saucer-type-deal called a Berg to take Thomas back to the WICKED headquarters so they can fix him up. Hey, WICKED didn't expect a gun to be in the Scorch, so that doesn't count as part of the trials.
Hmm, so WICKED said there were no rules, yet they just rescued Thomas because rules were broken. Strange.
Anyway, Thomas is dropped off with the group again, and they all make their way to the mountains. And whaddya know, Teresa is there with Group B, a bunch of girls who were also put through the Maze trials. Teresa isn't so happy anymore, and she seems to hate Thomas. In fact, Group B takes Thomas hostage: they walk away with him to kill him.
On their way to the place where he's supposed to be killed, Thomas talks the girls out of killing him. He thinks that WICKED is testing the girls' rational thinking as another Variable. The girls let Thomas go, but Teresa is not happy, and she storms away. Evidently, she wants this guy dead, so bad. She meets back up with everyeone when they're almost at the safe haven; there, she convinces Thomas to follow her, pleading that she was only acting mean.
Then comes her betrayal: she totally leads Thomas to a dark room, where he's supposed to be killed. She's been accompanied by Aris the whole time, and he's been communicating with her telepathically ever since they were put into the Maze. Ouch. Thomas is crushed. Turns out their mission was to kill Thomas the whole time.
Thomas is gassed in the room, but he doesn't die. In fact, his injuries from getting whacked on the head by Teresa's spear are cured, and she comes running into the room telling him it was all an act. The story goes that WICKED told her they'd kill Thomas if she didn't do what she was told; her mission was to make Thomas feel betrayed, or else WICKED would kill him.
Well, we're not sure what to think of that, but we can tell you one thing: boy, does this boy feel betrayed.
Thomas reluctantly follows Aris and Teresa so that they can reach the safe haven. He doesn't trust either of them, despite the fact that they seem like they're genuinely sorry for what they did. The three meet up with Groups A and B, who are standing over a stick with a flag that says "The Safe Haven."
With an hour left until the end of the trials, giant coffin-like containers suddenly descend from the clouds, and huge monsters climb out. Oh, brother.
Both groups are forced to fight the monsters, and there's basically an epic battle. A few Gladers die, but no one too important. Then when the trial time is up, another Berg appears, and everyone jumps on it. Finally, the trial is over.
Haha. Not quite.
A man who represents WICKED isn't too happy about the fact that Brenda and Jorge have made it onto the Berg, since they aren't test subjects. Oh, well—Thomas steals the dude's gun and forces him to let Brenda and Jorge stay.
Everyone's placed back in a dormitory again, except for Thomas, who finds himself in a plain white room. Teresa speaks to him telepathically, asking if he's okay. She tells him that everyone's been in the dorms for a week, but WICKED has been telling everyone that Thomas has the Flare, so he's being treated elsewhere. Thomas gets totally fed up with Teresa and tells her to go away, real mature-like.
Though she's hurt, Teresa consents, but she tells Thomas one last thing: "WICKED is good" (65.39).
The story ends there, but then the epilogue begins with yet another memorandum from Ava Paige, the Chancellor of WICKED. She says that things are going well despite a few hiccups, and the kids are all going to have their memories restored eventually.
Yeah, there's totally going to be another book.