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After Samus defeated Metroid Prime on Tallon IV by overloading it with the Phazon Beam, the creature began to destabilize, and in a desperate move, it absorbed her Phazon Suit and subsequently exploded. Little did Samus know that as she left the planet, a new enemy was born from her DNA and the remains of Metroid Prime. The Phazon Suit was a necessary piece of this fusion, as Metroid Prime had destabilized and no longer had a body. With its acquired human DNA, as well as the Phazon Suit as a body to construct itself into, it formed itself into a new enemy - the creature known as Dark Samus.
Search on Aether
Dark Samus, as it appears in Metroid Prime 2: Echoes
Dark Samus, now with a new form based on Samus' Power Suit and instincts that commanded it to absorb and spread Phazon, managed to leave Tallon IV in search of it in Samus's stolen Phazon Suit, though now black and dark blue in color with skeletal features and Phazon markings. Dark Samus eventually discovered the planet Aether, which was rich with Phazon. A Leviathan from Phaaze had landed on the planet fifty years prior, ripping open a second, darker dimension, Dark Aether. Dark Samus explored Aether and absorbed any Phazon it could find on the planet.
Pirate Raids
The Space Pirates, prior to Dark Samus' arrival, had established a base on Aether. Once Dark Samus arrived, they initially thought she was Samus Aran, but were perplexed as to its strange dark suit and its actions. It only raided their base to obtain Phazon, killing any who denied it. Some of their Metroid specimens were also reported as stolen, and the Pirates, having spotted it at one time near the containment tanks attempting to breach them, believed that this "Dark Hunter" was to blame for the theft. Dark Samus also destroyed their stealth generator in one of its raids, causing disastrous results for the Pirates.
Encounters with Samus
Samus Aran eventually landed on Aether to investigate a missing team of Galactic Federation Marines who had landed on the planet in pursuit of a Space Pirate starship. Samus first encountered Dark Samus in the marine base, where Samus followed it into a portal to Dark Aether. There, she found Dark Samus absorbing Phazon, with several shadowy creatures above which Samus would soon learn were the Ing. Dark Samus fired a shot at the Light Crystal that protected her from Dark Aether's poisonous atmosphere. With the crystal broken, the Ing stole most of Samus's abilities while Dark Samus fled. Samus escaped through the portal with only a few pieces of equipment intact. It was at first unclear if this meant that Dark Samus was working directly for/with the Ing Horde though it was only due to the Ing choosing to attack Samus over the far less vulnerable Dark Samus, as the former could not resist Dark Aether's atmosphere. A Pirate scout witnessed this encounter and believed that they were not allies, but foes. The Pirates then considered employing Dark Samus to kill the real Samus, with precious Phazon as a reward, though unfortunately they did not have time to put this plan into action.
Dark Samus engages Samus in the Agon Wastes.
The next encounter took place in the Agon Wastes, within the Pirate base. Dark Samus appeared in front of Samus, behind a locked gate, and left. Unable to bypass the gate, Samus explored the rest of the base and reached a room full of Phazon collected by the Pirates. There, Samus had her first battle with Dark Samus. Once Dark Samus was defeated, it began to destabilize and unleashed a massive Phazon explosion before collapsing and disintegrating into Phazon particles in the air.
The particles that Dark Samus transformed into managed to reach Torvus Bog. Samus saw the cloud transform into Dark Samus, though it did not fight Samus. Instead, it merely laughed maniacally and disappeared. Samus later saw the same cloud in the Sanctuary Fortress, and it once again transformed into Dark Samus. It then destroyed the bridge to the Sanctuary Fortress and left, forcing Samus to find an alternative route across the chasm.
Samus later saw Dark Samus in the Fortress firing at several Dark Pirate Troopers; this confirmed that the Ing regard it as an enemy and not an ally as thought at the beginning. It then disposed of them and began absorbing several canisters of Phazon (showing just what happens if Dark Samus is denied Phazon). Samus pursued her foe, cornering Dark Samus within an elevator and battling it once more. Samus defeated it once again and the doppelganger, losing stability in its body, allowed itself to fall off the top of the tower as a hasty retreat before Samus attempted to stop it.
Dark Samus and Samus face off as Dark Aether collapses around them.
Final Battle
Once Samus had defeated the Emperor Ing and absorbed the remaining planetary energy, Dark Aether became unstable and began to collapse. Samus, having only eight minutes to escape, hurried out of the Sky Temple and began moving toward the exit. However, her hopes of escape were crushed when Dark Samus appeared, blocking the exit with a Phazon wall. Due to the huge amount of Phazon that it had absorbed, Dark Samus had begun to deteriorate, causing its suit to become transparent and revealing its organs along with a humanoid skull with three yellow eyes inside its helmet. The eye on the back of its hand featured on the arm that reached out of the pool at the end of the first game was also rendered visible (though with a smaller pupil and yellow rather than blue).
Both Samus and Dark Samus engaged in a grueling battle, though Samus managed to defeat it once again by taking advantage of her foe's sole weakness: an overload of Phazon. Samus absorbed Dark Samus' Phazon into her Charge Beam, and shot it back. The attack penetrated Dark Samus's Phazon shield, and caused Dark Samus to destabilize, just as it had as the Metroid Prime, and it collapsed, defeated once again by its own attacks. In it dying moments, it painstakingly reached out in an attempt to touch Samus (possibly trying to absorb the Light Suit like it did the Phazon Suit), but de-materialized into a cloud of Phazon particles at the last second. Samus escaped Dark Aether and brought peace to the Luminoth on the planet, and it seemed that Dark Samus perished along with Dark Aether.
Yet, even though Dark Samus lacked a corporeal form, it still existed, and as shown in the 100% ending of Echoes, in which the Phazon particles again reform into Dark Samus's body, it would be only a small amount of time before it would return.
Return
Dark Samus at the beginning of Corruption.
Sometime between the events of Metroid Prime 2: Echoes and Metroid Prime 3: Corruption, the Galactic Federation, seeing great use for the mutagenic substance, took some of the Phazon from Aether. However, they left most of it behind, and the Space Pirate crew of the battleship Colossus soon collected the remaining Phazon. However, they would soon find out to their horror that they had unknowingly taken the particles of Dark Samus as well. Using the Phazon collected by the Space Pirates, Dark Samus regained its physical form (now with a more armored look, as opposed to its previously organic appearance) and wiped out a third of the Space Pirates aboard the ship. It then used its Phazon energy to brainwash the rest into accepting it as their new leader with the promises of incredible riches and power.
The Seeds of Scheming
With the Pirates so suckered into its schemes, a quasi-religious cult began to form around it and they followed its every whim. It taught the crew to turn the Colossus into a mighty Phazon-fueled craft. It then left them for several months to locate the source of all Phazon - the planet Phaaze. During its absence, its followers maintained order by executing those who doubted that it would return. During its journey, it encountered a Leviathan and used its energy to take control of it which led it to Phaaze. For Dark Samus, the chance to control the source of all Phazon was a chance to control the universe. Dark Samus absorbed a tremendous amount of Phazon, increasing its power to new heights. It then returned to the Pirates with the Leviathan and commanded them to follow it through the wormhole to Phaaze. She then revealed its plan to take control of the planet and to speed up Leviathan production, spreading Phazon strategically across the universe. How to do this was a dilemma, but a solution soon presented itself in the form of the Federation's Aurora Units.
Raid on the Valhalla
Under its orders, the Space Pirates attacked the G.F.S. Valhalla and stole the ship's Aurora Unit, 313. If the survivors of the raid expected mercy, they did not receive any. Under Dark Samus' orders, the Pirates jettisoned the survivors into the cold depths of space. The Aurora Unit was corrupted with Phazon and implanted into Phaaze, allowing Dark Samus to directly control the planet and all of its assets - including the Leviathans.[1] The first Leviathan that it controlled was sent to the Space Pirate Homeworld. According to Space Pirate Data, the Space Pirates on the homeworld that had not been brought under Dark Samus' control fought back against the Leviathan, but failed. All remaining Pirates were brainwashed. Dark Samus presumably also used 313 to infect the other Aurora Units (in particular, Aurora Unit 242 of the GFS Olympus and Aurora Unit 217 of Skytown, respectively.) with the Corruption virus.
The Invasion of Norion
Next, Dark Samus sent three more Leviathans to planets important to the Galactic Federation - one to Norion, containing the important Base Sector Zero; one to Bryyo, the Federation's primary source of Fuel Gel; and the last to Elysia, containing SkyTown, a vital research facility. Presumably, it also proceeded to cause an anomaly to Samus' cryostasis while the latter was on her way to Norion. While the Bryyo and Elysia Seeds collided without any trouble, Dark Samus encountered opposition on Norion - specifically, in the form of Samus Aran and three other Bounty Hunters: Rundas, Ghor, and Gandrayda. Just before they activated the cannon to destroy the oncoming Leviathan, Dark Samus confronted them, crashing through a window and repelling the Hunters' attacks with a Phazon shield. Despite the Hunters' efforts, she overpowered them and corrupted them with Phazon. Believing its work to be done, Dark Samus flew off, but Samus, using the last of her strength, managed to activate the cannon and destroy the Leviathan before falling unconscious.
After this, Dark Samus herself stayed on Phaaze and did not appear to the bounty hunters, busy performing their duties of destroying the Leviathans. However, due to its "mark of corruption" that it had left on all four of the bounty hunters, all but Samus succumbed to Phazon Corruption and became completely possessed by Dark Samus (this is most evident in the cutscene just prior to the battle with Rundas). Over the course of the game, Samus is forced to kill all three of them. Each time one of them dies, a shadowy apparition of Dark Samus appears before them, absorbing their bodies and their powers. This form is a black collection of smoke that has what may be tentacles acting as "wings". After each absorption, Dark Samus swoops down and flies away. This form depicts Dark Samus' visor.
The Final Confrontation
Dark Samus was confronted for the final time in its Sanctum on Phaaze, where it challenged Samus to a grand final battle. However, after being injured considerably, Dark Samus called forth the stolen Aurora Unit 313 and merged with it in a last-ditch effort to defeat Samus. After a grueling two-part battle, the Aurora Unit was destroyed, as a result, Dark Samus, the embodiment of phazon, was ejected from the Aurora Unit while exploding into Phazon dust with agonized cries and thus, was destroyed for good along with all phazon.
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