The Kill Order (Maze Runner Series, Bk. 4)

When sun flares hit the Earth, intense heat, toxic radiation and flooding followed, wiping out much of the human race. For Mark and his friends, surviving is difficult, and then an enemy arrives, infecting people with a highly contagious virus. Thousands die, and the virus is spreading. It's up to Mark and his friends to find the enemy - and a cure - before the Flare infects them all.