In Millennia you play a human who is snatched from his own space by a race called The Hoods, in order to take upon himself the mission of restoring balance to the dimension called Eschelon.
You are equipped with a time traveling, self-sufficient spaceship called XTM. Using it, you have to travel through time and establish the four indigenous species so that they're evolved enough to travel through space, all in an effort to stop the spread of the Viroid-Croids, or Microids in short, an evil and aggressive race with no regard for other lifeforms. Also, if you want to escape Eschelon, you will have to render the same four species evolved enough to generate replacement circuits for the ones damaged in your ship.
Your decisions will either get you out of Eschelon, destroy the Microids or, should you decide wrong, be the end of all life in Eschelon.