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.
The first two levels act as an introduction and allow the player to familiarize themselves with the controls. After that, Dr. Sepulveda begins assigning tasks that span several levels to achieve a long-term objective. The first task involves clearing the virus population from and reactivating the Mines and Power Generator to provide resources for the Construction Yard. Once done, the Yard begins producing armored units, allowing the player to move on. The next task involves the reincarnation of Darwinians: the Soul Repository in the center of Darwinia collects the floating souls, and sends them down to the Receiver, where the Darwinians collect them and send them to the Pattern Buffer to be reprogrammed with the main Darwinian blueprint code, where they are sent to the Biosphere to be reborn. The player must clear the Virii from and reactivate all of these facilities.
In the final level of the game, Dr. Sepulveda traces the Viral infection back to its source: E-mail spam. The Darwinians had managed to access Sepulveda's computer, downloading several files and eventually, the Spam. The E-mails were infected with a very nasty strain of internet virus which corrupted the Darwinians. The player is tasked to destroying the few remaining emails.
Darwinia does not fall into any one game genre, as it mixes elements from strategy, action, puzzle, hacker, and God games alike. Its retro styling coupled with colourful 3D design is unlike most games on the market. The player has the ability to run several programs through the Task Manager (a reference to the Windows Task Manager), similar to units used in many real time strategy games. Research allows the player to upgrade programs and weapons, which is critical as the enemy develops. Mission Objectives are given at each location/level, as the player and the Darwinians attempt to wipe out the Virii in a Great War.