- Sent to assist a Galactic Federation squadron stranded on the planet Aether, Samus Aran is thrust into an all-but-lost war between the dying Luminoth race and the umbral demons known as the Ing, on a world torn between light and darkness.
- While investigating a disturbance involving a Federation-led attack on the Space Pirates on the planet Aether, Samus Aran is thrust into a fierce war between the dying Luminoth race and their mortal enemies, the shadow-dwelling demons known as the Ing.—Anonymous
- Intergalatic bounty hunter Samus Aran has been hired by the Galactic Federation to solve the mystery of what happened to a group of Federation Marines, all of whom vanished on the planet Aether. When Samus arrives, she finds every one of the Marines dead, apparently slain by powerful, shadowy creatures-but in the middle of her investigation, she sees a figure that seems to be... herself, in a dark suit. Samus follows her double into a portal that leads to a world filled with the same shadowy creatures that the Marines' logs hinted at. Samus eventually learns of the evil that surrounds the planet. It would appear that a meteor carrying Phazon, the mutagenic compound that the Space Pirates were using on Tallon IV, struck the planet, creating a Dark Aether where an evil race known as the Ing were born. The Luminoth, wise creatures that lived on Light Aether, warred with the creatures, but they are being destroyed due to the Ing's theft of their own planetary energies. The Luminoth beg Samus for her help in restoring the energy and destroying the darkness for ever. Samus agrees...and a new adventure begins!—Anonymous
- In the Dash region of the Galaxy, the infamous bounty hunter Samus Aran has been called upon to locate the Galactic Federation Ship Tyr. The ship was in pursuit of a Space Pirate ship, and in their last transmission, the marines reported that they were following the Pirates to a planet called Aether, which is on the border of Federation territory. Since then, all contact with the marines has been lost. Samus has been asked to find out what happened to them. She travels to Aether with her domed ship, but during the attempt to land, the violent atmosphere disables the ship's controls, forcing her to make an emergency landing. She crashes the ship safely into a cave, but the extensive damage renders it unable to fly any longer. With auto-repairs of the ship expected to take a while, and the atmospheric circumstances making it impossible to contact the Federation with the ship's transmitter, she has no choice but to explore the planet.
The area is a large industrial complex from an obviously sophisticated civilization, but there is no trace of any inhabitants, only large insect-like creatures that burrow in the ground. Through a series of their tunnels, Samus gains access to several caves containing a rudimentary operation center. She finds most of the marines and several indigenous creatures, but they are all dead, with signs of gunfire. To her surprise, a few of the corpses are suddenly revived by a purple cloud, and they start to attack her. She defends herself and proceeds to a large open area. She locates the Tyr, which suffered a similar fate as her own ship. She discovers the rest of the marines dead as well, all spread around the ship, or their bodies taken within caves. By accessing their personal logs, she finds out that the marines were stranded and set up an emergency operation center inside a hive, but they kept enduring attacks from the insect creatures, which they called "Splinters". Despite attempts to eradicate the hives containing the creatures, they vastly outnumbered the marines and kept attacking until they ran out of ammo. Samus finds a video recording of the marines' last stand near the Tyr, where the mysterious purple cloud came out of nowhere, took over the Splinters, and killed the last remaining marines.
Further inside the complex, Samus discovers a mysterious gate which she can activate. She crosses the gate, and finds herself on a dark and twisted copy of the planet she just left. The atmosphere there is extremely corrosive, even for Samus' suit. Only nearby light crystals create safe zones where the atmosphere doesn't have any effects. To Samus' surprise, she suddenly sees a strange figure in front of her, drawing energy from a wall of Phazon. The figure turns around, and it looks like a dark copy of Samus herself. The evil twin is quite hostile, destroying a nearby crystal and exposing Samus to the harsh atmosphere. It doesn't take long before Samus is attacked by the same types of creatures that also killed the marines, but considerably larger. She stumbles back through the gate to her own world, but she finds out that the creatures managed to steal away most of her suit upgrades.
Samus continues her search, and finds a derelict structure called the Great Temple. She is attacked by one of the large dark insects, but she defeats it, and obtains an item called an Energy Transfer Module which binds with her suit. Further ahead she meets the guardian of the Temple, a benevolent being called U-Mos. He tells Samus that he is a Luminoth, an enlightened species that once settled on Aether. Their civilization had enjoyed peace and prosperity for centuries, until the planetary energy became unstable. So large energy controllers were constructed, to sustain the planet's energy and prevent the planet from collapsing. But then, decades ago, a large meteor impacted on the surface of Aether, and devastated large parts of the lands. However, the impact also created a dimensional rift, which split the planet in two separate worlds, existing in different dimensions; apart from Light Aether, a Dark Aether was born, inhabited by an evil species called the Ing.
It did not take long before the Ing created gateways to cross over to Light Aether, and waged war on the Luminoth. The Luminoth, in return, created portals and light weapons to bring the fight to the Ing. Although they fought bravely, they were vastly outnumbered by the Ing, who could take over other organisms and turn the Luminoth against each other. Many died during the ensuing war, so a new strategy was devised. Apparently, the meteor had also divided the planet's energy over the two planets; the Luminoth then tried to steal the Ing's half from their energy controllers, because when the energy on one world is depleted, then that planet will collapse and be destroyed forever. They traced the main energy controller on Dark Aether to the Sky Temple, the dark counterpart of the Great Temple, but it was guarded by the Ing leader, the Emperor Ing. To access the Sky Temple, the Luminoth needed to find and return the ten Sky Temple keys hidden throughout Dark Aether, but they failed. To make matters worse, the Ing then followed the same plan, and stole most of the energy from Light Aether. With their final hope gone, the remaining Luminoth, minus U-Mos, went into stasis, to be awoken in the unlikely event of their salvation.
The planet is now on the verge of destruction; however, Samus arrived and interfered before the Ing could steal the last remaining energy from the Great Temple. Samus' only chance for survival is to help U-Mos and save Light Aether. U-Mos instructs her to travel to Dark Aether and retrieve all the stolen energy with the Energy Transfer Module, as well as her stolen suit parts. She will need the nine Sky Temple keys to confront the Emperor Ing and obtain the final bit of energy. The toxic nature of Dark Aether's atmosphere, however, means that she can only stay there for short periods, and has to make use of Light zones created by the Luminoth's Light Crystals.
Samus goes on a search through the Wastelands of Agon, the Torvus bog and the Sanctuary Fortress, as well as their counterparts on Dark Aether, and finds all kinds of Luminoth items that help her in her quest, such as a Dark Suit that provides partial protection from the dark atmosphere. She also defeats several Ing that absorbed her suit upgrades, getting her suit back to full power. While searching for the keys and suit upgrades, Samus finds out that Light Aether has been invaded by Space Pirates, who sought refuge after their defeat on Tallon IV. They started to invade Dark Aether to mine Phazon, which is abundant on Dark Aether as well, and they are experimenting with Metroids again. And to make things worse, Dark Samus is actively roaming the land as well, hungry for the mined Phazon and growing stronger by the minute. Samus encounters her two times throughout her search for the missing energy. In both instances, she defeats and destroys her, but Dark Samus' particles are able to reform each time; only a subatomic explosion could completely destroy her.
With each conquest made by Samus, the Ing start to get more aggressive, up to the point where they even possess Luminoth machines and the Space Pirates in an attempt to stop her. Samus' quest is helped by a Light Suit, which is impervious to the toxic atmosphere of Dark Aether. She defeats all the large guardians of each area, and retrieves all the lost energy and the keys, giving her access to the Sky Temple. There she encounters the huge Emperor Ing. After a fierce battle, she defeats it and retrieves the last bit of planetary energy. Immediately, Dark Aether becomes unstable and starts to shake violently. Samus tries to get back to a portal before the planet collapses, but is stopped by Dark Samus, now no more than a regenerated skeleton. They battle again as the clock towards planetary destruction counts down. Finally, a Phazon-fueled arm cannon is used to get the fiend to her knees. Dark Samus makes one final attempt to grab Samus, but she disintegrates into particles again before she can lay her hand on Samus. Samus escapes through the portal, and Dark Aether collapses behind her, destroying all the Ing with it.
Samus restores the last of the planetary energy to the energy controllers, and Light Aether is safe again. Samus is saluted as a hero by U-Mos and his fellow Luminoth, who have been revived. She enters her repaired ship, and leaves the planet to her next destination, not seeing how Dark Samus is reforming again in space...
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