Darwinia was created as a digital theme world for artificially intelligent polygons by Dr. Sepulveda. Housed in a massive network of surplus Protologic 68000 machines from the 1980s, Darwinia is a world where the single-poly Darwinians, with their simple, but growing AI, can grow and evolve. Darwinia is also where the world can visit to see them frolicking in their natural, fractal habitat. Darwinians live a life, working and growing, until eventual death, which releases their digital soul to be reincarnated.
However, the player arrives in the midst of an emergency. Darwinia has been infected by a virus, and Dr. Sepulveda is near panic watching decades of research being corrupted and consumed. Sepulveda enlists the player to aid him in rescuing the Darwinians and drive off the virus. The player is given access to the combat programs, simple tools that originally began as mini-games, but now are the only means of attack against the virus. As the player progresses, it soon becomes clear this is not enough, and that triggers the third aspect of the gameplay - evolution.