The plot of the game is brilliant. Your enemy is an evil alien race called Microids. To beat them you must travel back in time 10,000 years and - like a god - take care of 4 different races so that they grow, develop and become powerful civilizations. You will communicate with the four races (Reptoids, Slothoids, Entomons, and Piscines) using a "seed". You will need to guide them, protect them if necessary, and help them grow until they can eventually colonize other planets.
This way, you will change the timeline - and you will be able to monitor the changes happened to the history using your computer. If you succeed, the Microids will be defeated, and the four races will also help you return to your time repairing your ship's components.
The game didn't have a huge success, and some reviews were negative due to some bugs. Despite this, Millennia is a unique game with a fantastic plot and different mechanics. If you love the idea of time manipulation, you cannot miss it.