Thomas and Minho escaped, Newt got fixed, they all went their separate ways. Harder for WICKED to track them that way.
Only, WICKED manages to, dragging Thomas back to the maze, wiping his memory clean of anything that isn't strictly WICKED. After four years, WICKED puts all the surviving candidates back in the maze, still testing their brain-responses, still looking for a cure.
But not for the flare.
For the supernatural.
--- "And please, for all that is still good, remember WICKED isn't good." ---
• I do not own any of the characters from Teen Wolf or The Maze Runner, all rights go to Jeff Davis and James Dasher •