Dark Samus emerges as the main antagonist in the Metroid Prime series as the series progresses. Dark Samus is, in actuality, Metroid Prime, who Samus Aran first encountered in the impact crater of Tallon IV in the first Metroid Prime game. After suffering a defeat at the hands of Samus, Metroid Prime, an unknown alien who drew strength from Phazon, ripped the Phazon Suit enhancement from Samus's power suit. With this imprint and the corrupting power of Phazon, Metroid Prime was reborn as Dark Samus, a Phazon entity in Samus's image.
Dark Samus, being an entity consisting entirely of Phazon, is utterly reliant on the substance to survive and grow in power. The raw power of Phazon, combined with Metroid Prime's ability to absorb life essence, makes Dark Samus an extremely dangerous foe. Destroying Dark Samus's physical body causes it to destabilize and dissolve into Phazon particles, but if and when it is able to find raw Phazon to absorb, its essence can always rebuild itself.
Samus first encounters Dark Samus in Metroid Prime 2: Echoes on the planet Aether. There, she finds Dark Samus feeding off the Phazon that is corrupting the planet and tearing it between two dimensions. Samus defeats her nemesis several times, finally destroying her physical form in Dark Aether before it is wiped from existence due to Samus's efforts to restore Light Aether's power. Dark Samus was not destroyed entirely, however, and its essence returned with Samus to Light Aether, able to make its way to the Space Pirate vessel above the planet and feed off their stored Phazon reserves until it was able to re-assume its physical form.
By Metroid Prime 3: Corruption, Dark Samus gains the ability to control those under what is known as Phazon Madness, a condition that deteriorates the mind of the victim, making them extremely powerful and violent and shortening their lifespan. Through this power it is able to corrupt the Space Pirates into aiding it in its plan to spread Phazon corruption throughout the entire galaxy. It makes them attack the Galactic Federation starship, the GFS Valhalla, in order to steal Aurora Unit 313 and bring it to the planet Phaaze, the homeworld of Phazon, where Dark Samus corrupted it and installed it into the living planet, allowing it to directly control the planet and the Leviathans that would spread the corruption of Phazon.
At the beginning of Metroid Prime 3, Dark Samus attacks Samus and her fellow Hunters, Rundas, Gandrayda and Ghor, leaving its corruptive mark on them all, causing their bodies to naturally produce Phazon, eventually leading to Phazon Madness and coming under the control of Dark Samus. Rundas, Gandrayda and Ghor all succumb to Phazon's corrupting influence, eventually having their essences absorbed by Dark Samus after their defeats at the hands of Samus. If players allow Samus to succumb to Phazon Madness by abusing Hyper Mode and causing a Phazon overload, she will also become corrupted, leading to an alternate game over screen where she transforms into a doppelganger of Dark Samus.
In the closing minutes of Metroid Prime 3, Samus faces her nemesis in an intense battle on the planet Phaaze itself. Dark Samus melds itself with the stolen Aurora Unit and is eventually defeated by Samus, causing Phaaze to destabilize and explode, destroying all Phazon in the universe. Without Phazon to absorb to resurrect itself, Dark Samus is finally destroyed once and for all.