Following the evacuation of Big Boss and Kazuhira Miller from the besieged Mother Base, a wormhole opens in the sky and absorbs the offshore plant as well the remaining MSF soldiers. The soldiers are transported to an alternate reality along with the remains of Mother Base, to find the world full of hostile, crystalline zombie-like entities known simply as creatures. Their goal is to find materials and do anything they can to just go back to their own world. In order to find these materials, the survivors must work together to kill the creatures and explore around their surroundings.