At the end of the first movie Thomas and his group were seemingly saved by a group of soldiers from the facility they were being kept in. But the place they are taken to, on the outskirts of a desert, is even worse. This is where they not only create the monsters encountered in the Maze, but use the teenagers to produce a temporary serum for the virus that's transforming humans into these weird zombie-like creatures. In doing this, they put them in a vegetative state and hang them on racks. Thomas and his friends escape out into the desert and eventually find themselves in a blasted-out looking city. They even cross part of the ocean that is now desert. All the water seems to be gone. And yes, they encounter the vicious zombies. Eventually they come across other survivors, the last of which is a group run by Barry Pepper (the lead in BATTLEFIELD EARTH). But one of their own betrays them-and the evil men from the facility show up.
Overall I like the MAZE RUNNER flicks better than both the HUNGER GAMES and DIVERGENT series. It's a lot along the lines of a light version of RESIDENT EVIL.