Dystopian Literature
Yeah, we've already established that The Maze Runner series is dystopian, but it's important to acknowledge that this is the third book in the series (and last book of Thomas's story), so it also has a dystopian ending.
Dystopian endings are almost never happy. In fact, they're usually a whirlwind of emotions: readers often feel sort of happy—but also extremely sad. We mean, okay, yeah, some of our heroes have survived, but the world is ending. Sort of. Even if some people are happy, most people are dead.
We'll get into all of this more in the "What's up with the ending?" section.