Unfortunately, E-DNA proved to be unstable. All of the test subjects who came in contact with it were transformed into uncontrollable genetic mutants soon named "The Darkspore". Fearing these new creatures, the Crogenitors threw Xylan into exile for his behavior and negligence, outlawing the use of E-DNA. Xylan faked his death and went into the hiding. Believing himself able to control the power of E-DNA, he injected it to himself. This act transformed him into the Corruptor—a mentally unstable, yet extraordinarily powerful, mutant who can master all Darkspores. Determined to get revenge on the other Crogenitors and conquer everything, he gathered allies, formed an army of mutants, and strengthened the E-DNA mutagenic power. Afterwards, the Corruptor began conquering the planets of the Crogenitor empire, infecting them through the use of E-DNA bombs, and destroing Crogenitor fortresses with his mutants and war machines.
The first planet to fall was Zelem's Nexus, home of the most brilliant Crogenitor scientist, Zelem, and key planet of the Crogenitor empire, rapidly followed by many others. During the Mutation Wars, almost all genetic heroes were slaughtered, the majority of all Crogenitors were killed, and the Crogenitor empire dissipated, star by star. Retreating to their capital planet Perceptum, as a desperate plan, the Crogenitors put selected companions into enormous laboratory cryoships and launched them into space luckily undetected, mere minutes before the Corruptor's final exterminating campaign. Awaiting the moment when one of the HELIX A.I. networks installed aboard each starship would complete the stabilization of the E-DNA, the surviving Crogenitors slept indefinitely. After 1000 years of calculation, the HELIX aboard one of those spacecraft succeeded. Awakening the survivingCrogenitor that was carrying, the HELIX informed the slightly amnesiac Crogenitor about the plan to free the galaxy: gather the best surviving genetic heroes then strengthen them with the power of the stabilized E-DNA, forming the "Crogenitor Insurgency".
As the game begins, the player takes on the role of this Crogenitor. Starting with only a few brave heroes, the player goal is to purge the Darkspore from the galaxy planet by planet, moving ever closer to your ultimate goal of destroying the Corruptor forces.
In the end, after building your army of genetic heroes and eliminating Darkspore on each of the base planets, the Corruptor's hideout is located on the ruined desert planet of Perceptum renamed "Scaldron". Ultimately, the Corruptor is defeated, and exploding into a burst of white light. After his demise, all that remains of him is the mask of Xylan, laying lifeless on the ground.
In the closing moments of the game, HELIX then informs the player that without their leaders, the Darkspore forces are splintering and the other surviving Crogenitors are completing the work of restoration; life is returning to normal on the various planets that the Player have aided. After this, the game zooms back down to Scaldron and shows Xylan's mask on the ground. HELIX then calculates the probability of Xylan resurrecting, and gets 0.00832%, but then corrects herself after a short moment, and instead, comes out with 0.00833%. Right before the screen fades to black, one of the eye holes on the broken mask begins to glow red before flickering back out...
