Bacterial Takeover is set in a fictional Universe. Some of the [[Planets|'''planets''']] are the same as in our Universe, like Mercury and Mars, or Earth, which even has a population that is roughly similar to our world.

Many of the planets that the player visits at some time have been inhabited by various civilizations, such as planet '''Atreria''' and '''Dospunus'''. Some parts of planet descriptions can change after entering a '''[[Black Hole]]''', which sends the player to an alternate timeline.