Civil Protection Unit 3650—Aiden Walker—was pulled from active duty and reassigned to an offsite team following an incident involving several other CP units. That event formed the basis of the original Entropy: Zero. In the sequel, Walker is brought back as an Overwatch Elite. His willpower and faculties have been restored, and he is believed to be the last surviving copy of himself. His new directive: capture Dr. Judith Mossman and discover what she is searching for.
While Half-Life 2 used City 17 and its coastline as its backdrop, Entropy: Zero 2 unfolds primarily across frozen tundras and mountain ranges—the same remote terrain where the research vessel Borealis was hinted to be located, a connection supported by a brief "B" visible in reference footage matching the name "BOREALIS" found stenciled on a cargo ship's hull. Three endings and a secret fourth are available, each shaped by choices made throughout the final chapter.