In an alternate plot of the movie, two Colonial Marines are sent to the USS Sulaco to rescue survivors only to crash land on Fiorina "Fury" 161. After fighting a Super Facehugger, they discover that Fiorina has been infested by hundreds - possibly even thousands - of Runners. They kill countless of the Xenomorphs, rescuing prisoners until they meet the Aliens' "big boss". The Marines destroy the planet's defense systems, programmed by Weyland-Yutani. They eventually kill the Big Boss; later they meet "An Unidentified Man", who asks them about "biological samples" (the Aliens). After learning that all of the Aliens were killed, he attacks the Marines but is killed. A squad of numerous Weyland-Yutani soldiers then confront the Marines and the game ends as the soldiers open fire on the Marines.
The records of the incident on Fury 161 was removed, and the facility there was closed and almost all was forgotten. The USCM removed two names from the Colonial Marine ranks (the two players) who are M.I.A., as no one knows if they're dead or alive.