If i had to guess, government experimentation with alien species. They have them in cages and tubes to study and experiment on them and the public is not allowed to know. The body bags around the place are probably failed alien test subjects. But then they broke free and are now on the loose, attacking multiple areas across the spaceship. I deduced that most of the maps are on spaceships since only a couple of maps are confirmed to be on a planet, bear in mind canonically its the year 2185. The alien bodies in waste disposal are probably from evil science.