After Samus defeated Metroid Prime on Tallon IV by absorbing Phazon and using it as a weapon against it, the creature began to destabilize, and in a desperate move, it absorbed her Phazon Suit and subsequently exploded. As Samus left the planet, a new creature was born from Samus' DNA and the remains of Metroid Prime, using Samus's Phazon Suit as a shell - the being known as Dark Samus.
Metroid Prime 2: EchoesEdit
Dark Samus, now with a new Chozo-based shell and instincts that commanded her to absorb and spread Phazon, managed to leave Tallon IV in search of it in a suit similar-looking to Samus, although with skeletal-looking feet, crystal-like shoulder pads, and a more menacing overall figure. She eventually discovered the planet Aether, a planet rich with Phazon. A Leviathan from Phaaze had landed on the planet fifty years prior, ripping open a second, darker dimension. Dark Samus explored Aether and absorbed any Phazon she could find on the planet.
The Space Pirates, prior to Dark Samus' arrival, had established a base on Aether. Once Dark Samus arrived, they first thought she was Samus Aran. Her dark suit and her forceful invasions to obtain Phazon confused them, and they also found strange the fact that she began freeing the Metroid specimens instead of killing them. As Dark Samus was once a Metroid (or perhaps still contained some Metroid DNA within from her previous forms), she most probably pitied the trapped specimens and felt as having a close bond with them. The Pirates began to refer to her as the Dark Hunter.
The real Samus eventually landed on Aether to investigate what had happened to a team of Galactic Federation marines who had landed on the planet in pursuit of a Space Pirate frigate. Samus first encountered Dark Samus in the marine base, where she followed her into a portal to Dark Aether. There, she found Dark Samus absorbing Phazon, with several shadowy creatures which Samus would soon learn to know to be the Ing above. Dark Samus, sensing her, 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 power-ups. She escapes 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 may only be due to the Ing choosing the more vulnerable Samus over Dark Samus, who could resist Dark Aether's atmosphere.
The next encounter took place in the Agon Wastes, within a Space Pirate base. There, Samus had her first battle with Dark Samus. Once Dark Samus was defeated, she began to destabilize and unleashed a massive Phazon explosion before collapsing and disintegrating into Phazon particles in the air. Samus believed that her foe was dead after the encounter.
However, this was not the case. The particles that Dark Samus transformed into managed to reach Torvus Bog. Samus saw the cloud transform into Dark Samus, though she did not fight Samus. Instead, she merely laughed and disappeared. Samus later saw the same cloud in the Sanctuary Fortress, and it once again transformed into Dark Samus. She 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 firing at several Dark Pirate Troopers; this confirms that the Ing regard her as an enemy and not an ally as thought at the beginning. She disposed of them and began absorbing several canisters of Phazon. Samus pursued her foe, cornering Dark Samus within an elevator and battling her once more. Samus defeated her once again, and she fell off the top of the elevator and again disintegrated.
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, Dark Samus suddenly appeared, blocking off the escape route and forcing Samus to battle her again. Due to the huge amount of Phazon that she had absorbed, Dark Samus had begun to deteriorate, causing her suit to become transparent and revealing her organs along with a bizarre, three-eyed face inside her helmet, revealing her to be the reborn Metroid Prime. Another eye appears on the back of her hand, similar to the arm that reached out of the pool at the end of the first game (though with a smaller pupil and yellow rather than blue; why and how these changes occured in uncertain, although it may just be a random mutation resulting from the massive quantities of Phazon she had consumed by that time). It is interesting to note that her "organs" are actually energy-based, and are shaped in galaxy spiral-type shapes in various colours. It also appears that she has a skeletal system, albeit shaped like Samus's suit.
Both Samus and Dark Samus battled in two phases, though Samus defeated her once again. During the fight, Dark Samus tried several times to kill Samus by launching pure Phazon at her, but Samus absorbed the 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 she had as the Metroid Prime. She tried one last attempt at defeating Samus by trying to absorb Samus's Light Suit, but disintegrated just before she touched her. Samus escaped Dark Aether and brought peace to the Luminoth on the planet, and presumed that Dark Samus died along with Dark Aether.
Even though Dark Samus lacked a physical form, she still existed, and it would be only a small amount of time before she would return.
Metroid Prime 3: CorruptionEdit
Sometime between the events of Metroid Prime 2: Echoes and Metroid Prime 3: Corruption, the Space Pirates briefly returned to Aether to collect the small amount of Phazon that remained, just before the Galactic Federation came and took the rest of it. In their haste, however, they also collected the particles of Dark Samus. Using the Phazon, she regained her physical form (now with a more armored look to it) and wiped out a third of the Space Pirates aboard the ship. The rest were brainwashed into accepting her as their new leader.
Soon after Dark Samus had established her followers, she left them for several months. When she returned, she brought with her a Leviathan - she had managed to find the planet Phaaze. Bringing the Space Pirates back with her, she began her mission to spread Phazon across the universe.
Under her orders, the Space Pirates attacked the GFS Valhalla and stole the ship's Aurora Unit, 313. The Aurora Unit was corrupted with Phazon and implanted into Phaaze, allowing Dark Samus to control the planet and all of its assets - including the Leviathans. The first Leviathan that she controlled was sent to the Space Pirate Homeworld, bringing all remaining Pirates under her control.
After this, Dark Samus sent three more Leviathans to planets important to the Galactic Federation - one to Norion, containing an important military base; one to Bryyo, the Federation's primary source of Fuel Gel; and the last to Elysia, containing a vital research facility. While the ones on Bryyo and Elysia 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, and, after a brief skirmish, corrupted them with Phazon. Believing her work to be done, Dark Samus flies off, but Samus, using the last of her strength, manages to activate the cannon to destroy the Leviathan before falling unconscious.
After this, Dark Samus herself does not appear until the game's climax; however, due to her "mark of corruption" that she had left on Samus, Rundas, Ghor, and Gandrayda, the latter three succumb to Phazon. 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.
Dark Samus was confronted for the final time in the depths of Phaaze. Dark Samus then challenges 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 is destroyed, and because it is linked to Phaaze's core it began a chain reaction that would culminate in Phaaze exploding, eradicating all Phazon from the universe. As a result, Dark Samus once again destabilizes, but this time is completely destroyed in a burst of Phazon.
If Samus were to succumb to the Phazon corruption inside her, she transforms into what appears to be a new Dark Samus, or something resembling it, leading to an alternate Game Over screen.
As Dark Samus, the creature utilized many abilities similar to Samus, in more powerful forms. It could fire Phazon beams at enemies in the form of small shard-like bursts (dubbed by fans as the "Shrapnel Beam") and use Phazon-charged Super Missiles to blast opponents into bits. She could also do a powerful dive bomb attack (which could be a Phazon based Screw Attack), a Phazon Boost Ball that generated vast amounts of kinetic energy in alarmingly short times, raise pillar-shaped shields of pure Phazon energy in this form, is capable of both flight and levitation, and can render herself invisible. However, when Dark Samus consumed too much Phazon, she gained the disadvantages she had in her previous form: Phazon fired at her could overload and destabilize her, resulting in her generating very powerful Phazon attacks to discharge the used Phazon radiation from her body, including a pure beam of concentrated Phazon.
In Metroid Prime 3, Dark Samus' abilities were further augmented. In addition to most of her previous abilities, she could now produce clones of herself (fittingly called "Dark Echoes") and is much more resilient to Phazon attacks (though Hyper Missiles are still effective on her). After she unleashed the massive blast of Phazon at the four hunters, the corruption within them seemed to be connected to Dark Samus; after the defeat of each hunter, a strange black wraith-like entity in the shape of Dark Samus would appear above the hunters, and fly off into space, presumably back to Dark Samus herself. This seems to be the manner through which she gained the Hunters' abilities--Gandrayda's agility, Ghor's Plasma Beam and ability to merge with machinery (the Aurora unit), and Rundas's ice pillars, to name a few.
Dark Samus is a very durable life-form, surviving a massive destabilization, and traveling unaided through space and freely between the Dark and Light Dimensions. She can survive in the vastness of space, travel through it, and live through the explosions of planets, even dimensions. This is how she has constantly been able to regenerate itself after defeat and fly to another planet for Phazon absorption. Metroid Prime 3: Corruption reveals her to be sentient and capable of long-range planning, as noted through a series of Space Pirate data logs that record the fanaticism she inspires among the mind-warped pirates. They detail her plans and how she reacts to certain events, and credit her with being something near a deity whose rule of the galaxy will be great. She might have been Samus' most powerful opponent.
Super Smash Bros. BrawlEdit
A "Dark Samus" appears in Co-op Event Match 7: Battle of the Dark Sides. This one looks more like the Zelda series's Dark Link (who she is partnered with), in that the character is only a black silhouette of Samus.
- Since Dark Samus is made up of Metroid Prime and Samus's DNA, Dark Samus can be considered Samus's daughter.
- Contrary to popular belief, Dark Samus is not weak against the Light Beam nor strong against the Dark Beam as she a Phazon-based life-form and is, therefore, of neither Light or Dark origins.
- Dark Samus appears as a trophy with her appearance in Metroid Prime 2 in Super Smash Bros. Brawl. Interestingly, even though it was canonically proven that Dark Samus was a reincarnation of Metroid Prime, her trophy states that there are many theories as to her origin, but none of them were proven.
- In each of her physical appearances, resemblances to Metroid Prime are visible. In Metroid Prime 2: Echoes, Metroid Prime's face and organs can be seen inside her in the final battle. In Metroid Prime 3: Corruption, her chest area is an alteration of Samus' that resembles Metroid Prime's face. Interestingly unlockable artwork in Echoes depicts her as having organs similar in shape and look to spiral galaxies.
- When Samus fights Rundas, she actually sees Dark Samus inside of him, an event which mirrors other scenes of the same type from The Matrix or Metal Gear Solid.
- Due to Dark Samus' origin, some fans have speculated that, technically, Dark Samus is a Metroid. A Space Pirate log in Metroid Prime 2]] seems to support this theory, as it counts an event in which Metroids were liberated by Dark Samus, confirming some sort of link with the species. It is also interesting to note that both Samus and Dark Samus both have Metroid and Samus' DNA (though the former didn't at the time of the latter’s existence).
- Dark Samus is one of two antagonists in the Metroid series that is known to have Samus' DNA, the other being the SA-X.
- According to promotional storyboard designs, the scene where Dark Samus points her Arm Cannon and fires Phazon at Samus in their first encounter in the beginning of Metroid Prime 2: Echoes is based off of the climax of Aliens.
- In Metroid Prime 2, Dark Samus seems to be incomplete, this is supported by the fact that she needed to constantly absorb Phazon, looks slightly deformed, and has a range of dangerous and random attack moves. In Metroid Prime, Metroid Prime's tentacle was broken off of Samus prematurely, possibly not absorbing enough DNA to create a whole, stable Dark Samus. In Metroid Prime 2 cutscenes Dark Samus seems to act almost mentally unstable, and becomes literally unstable due to constant Phason absorption. Dark Samus being incomplete also seems supported by the fact that, in Metroid Prime 3, Dark Samus does not need to absorb Phazon, acts calmer, and attacks in a more organized, orderly method. Being mentally stable also explains how she was able to brainwash the Pirates, plan the coordinates of the Leviathan impact locations, and steal the Aurora Unit.
- In all of her appearances, she is accompanied by a consistent theme song, entitled Darkness. The song is replaced by a remixed version in Metroid Prime 3: Corruption and was renamed simply "Dark Samus", but largely stays the same, melodically, and notes of it can be heard during Dark Samus' attack at Norion. At the end of Metroid Prime 2, however, the escape theme was played, because of the timer. It is interesting to note that the theme is present, although to a less extent, in the First Phase of the Aurora Unit battle, and is arranged in a way that resembles the theme of Mother Brain in Metroid Zero Mission.