Let's take a step back: before Thomas, there was Mark.
Right from the beginning, we're told that the story takes place thirteen years earlier than the Maze. So we have a bunch of new characters to get to know. There's Mark, Trina, Alec, Lana, Misty, the Toad, and Darnell. They're all survivors of the sun-flares, and they're living together in a village somewhere.
The conflict begins when a Berg shows up at the settlement—that's right, a Berg (a giant airship that WICKED uses back in Book Two and Book Three of the series—it's basically a plane, but with more rooms). It's super-rare for a Berg to show up, and the people who come out of the Berg shoot up the village with darts. People drop like flies (including Darnell), but Alec, Mark, Trina, Lana, Misty, and the Toad escape. Phew.
Amid the shooting, Alec takes out a grappling hook (from who knows where) and shoots it onto the Berg. Mark follows suit with another grappling hook, and pretty soon the two are walking around in the Berg trying to figure out what's going on. Alec and Mark break down some doors and generally cause mayhem, and pretty soon the Berg crashes.
Don't worry: Alec and Mark are fine. But when they trek back to the settlement, they find people dead everywhere. Oh, and Darnell is locked up in a cage going nutso. He's screaming about something hurting in his head. Then he—gulp—whacks his head on the wall until he dies.
So something bad is going on, clearly. Whatever was in those darts is poisonous, and it's spreading. The remaining friends decide to flee the village. On their way, though, Misty starts feeling sick. She's pretty much a goner too at this point, and the Toad refuses to keep going without her. Oh well: Trina, Lana, Alec, and Mark keep going.
About a few miles into the woods, the group stops to get some rest. As Mark is about to fall asleep, he sees the Toad in the woods. And as you can imagine, the Toad's now sick too. He tells them he took care of Misty until she died, and now his head hurts. Alec, being a grizzled war vet, takes the Toad out to the woods and kills him (we don't know how)—they can't have anyone with the virus following them.
We're down to Mark, Alec, Trina, and Lana. They start exploring the woods and come across another settlement. There, they find a little five-year-old girl who has a dart wound on her arm, but she's not sick. She tells them that her name is Deedee, and they decide to bring her with them. (Cause why not, right?)
By the way, let's take a break and talk about Mark. Whenever he dreams, the dreams are all very linear: they start at the day the sun-flares hit until the day that he escapes New York by boat.
Okay, we're back. So the group, now with Deedee, starts to move away from the settlement. But pretty soon they hear singing and see dancing out in a clearing. Mark and Alec take a gander, but the people see them and hold them captive. Great. Oh, and these people are big on praising spirits and condemning demons—they're nuttier than a Payday bar.
Alec and Mark are able to escape, but when they run away they realize the forest is on fire. Awesome. After lots of running (and making sure they don't get burned, natch) they get back to where they left Trina, Lana, and Deedee… and realize they're gone. Their week is just getting worse and worse.
Their next step is to find their friends, but on their way they stumble upon a landing pad for a Berg. It turns out that the landing pad leads to an underground bunker, where Alec and Mark find a group of crazy people yelling in an auditorium.
After some eavesdropping, Alec and Mark find out that the people in the auditorium were the ones who shot the darts at both settlements, but they aren't happy. Their superiors are in Asheville attempting to use a Flat Trans (a teleportation device) to get to Alaska. We're not sure why they want to go to Alaska at this point, but we can assume it's because Alaska is going to be the only safe haven left, seeing that Asheville is now filled with people infected by the Flare.
By the way, the people in the auditorium are suffering from the virus. Unfortunately for them, the virus is super contagious, so by shooting it and spreading it among the masses, they all accidentally caught it themselves. As you can imagine, they were fiddling with the darts while loading their guns—also, the Flare is something you can catch just by breathing in infected air. Basically, they had to do the dirty work for their superiors, and by doing the dirty work, they're now all doomed because they caught the virus. We'd be pretty ticked off, too.
Although they try to be stealthy, Mark and Alec aren't great at eavesdropping. Pretty soon, everyone in the auditorium thinks there are "spies," possibly working for the PFC (Post-Flares Coalition) listening in on them. Alec and Mark escape with a Berg (score!) but Mark realizes he has the Flare after torturing an attacker. Yeesh.
When Mark and Alec land, they're in a cul-de-sac outside of Asheville. Alec also did some reconnaissance in the area, and saw Lana, Trina, and Deedee being held captive by some crazies. So the next plan: save them somehow. Luckily, Mark and Alec find a weapon inside the Berg that dissipates people—it blows them to little pieces, causing their bodies to disappear into thin air. Awesome.
Alec and Mark fly the Berg to where Trina, Lana, and Deedee are, and they enter the area looking like the Ghostbusters. They're totally geared up because it's a zombie-land in that place. People attack them left and right, but Mark and Alec fend them off with their weapons.
Eventually, after approximately a million attacks and close calls, Mark and Alec find Lana. But she's stabbed by some crazy dudes, and Alec puts her out of her misery by shooting her with his weapon. Great. This story just keeps getting sunnier.
Fortunately, Mark and Alec find Trina and Deedee in a basement of a house. Unfortunately though, Trina is super-sick and doesn't even remember Mark. But since people are attacking them, they fight their way out and get to the Berg.
At this point, Trina's sick, Mark's getting crazier, and now Alec is feeling terrible. They all have the Flare, but Deedee's still fine. How is she managing it?
The plan now is to get Deedee to the Flat Trans in Asheville because she must be immune to the Flare—the problem is that this is a suicide mission for Alec, Trina, and Mark. But again, it's about all they can do. So that's what they end up doing; they get Deedee to the Flat Trans, then after she travels through it, Alec crashes the Berg into the building that has the Flat Trans, killing everyone.
But hey, at least Trina remembers Mark at the very last moment.
In the epilogue, we get to see the scene where Thomas is taken away from his mother. It's sad. :(
Then after the epilogue, we get a secret file that reveals Teresa's memory beginning in WICKED's headquarters. Turns out her name used to be Deedee—who woulda thunk it?