New York; Asheville, North Carolina; Alaska
It's not the New York we know today. The world is a pretty dismal place after the sun-flares, and you can pretty much imagine every location as being in the beginning stages of turning into the Scorch—the city we learn to hate in The Scorch Trials.
New York is where our main characters lived before the whole sun-flares fiasco. Then, it was pretty much the same as we know it today, except more advanced. But when the sun-flares hit, it became the lost city of New York:
But Manhattan has turned into a grid of rivers and streams, the fierce sun constantly reflecting off the waters in spectacular and blinding flashes. (46.8)
Yuck. That almost makes us feel affectionate toward the New York of today—rats, weird dudes on the subway, and all.
For the most part, Asheville is where most of the book takes place… although we tend to hug the fringes of Asheville rather than spending time in the middle of the city.
We don't get the exact location of the main characters, but they're able to fly to Asheville very quickly when they find the Berg, so we can assume they're somewhere in North Carolina. It turns out that Asheville is one of two places (Alaska being the other) in the U.S that became a safe haven after the sun-flares. To protect its citizens, gigantic walls were erected on the outside.
It seems like these walls were pretty flimsy, however. At the end of the book, Bruce and his friends can be seen charging the government building that houses the Flat Trans. We're not construction workers or anything, but it seems like the walls didn't do much to stop Bruce and his people from breaking into the city.
It's cold. It's full of adorable husky puppies. It's where WICKED's headquarters is located. It's Alaska.