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Metroid Prime: Episode of Aether is a manga series based on the events of Metroid Prime 2: Echoes that spans seven issues of Comic Bom Bom in Japan. Bom Bom is a monthly magazine published by Kodansha. This series was written by Matsumoto Hisashi from issue July 2005 to January 2006.
July 2005 issue of Comic Bom Bom, with Samus Aran in the upper right corner.
The Metroid Database, until February 2011, had 2 volumes on their website in their original format, with the first poorly scanned. They had announced they would not translate it until they had the rest of the chapters with the first being rescanned. As of February 2011, the first chapter has been translated.
Plot
Chapter 1
The story begins showing a transport and passenger ship, the Crest, under Space Pirate attack. Eight people are currently on the bridge when a large Pirate general harms a child hugging who may be his little sister. The Pirate general ridicules the child's hope that someone will help them when he receives a report that his ship has exploded. He then sees a famous gunship intervene, and is shocked to witness the arrival of the galaxy's greatest bounty hunter: Samus Aran.
Samus sends a report while the Pirate assumes that she is just one bounty hunter, and Samus is soon surrounded by thousands and thousands of Pirates. As always, she proves their beliefs wrong by leaping over them and annihilating most of them with a single blast. Samus then collects a machine gun left on the floor and fights the remaining Pirates with double the weapons. The Pirates are killed very quickly, and the general threatens the lives of an adult and child survivor. Samus manages to trick him into letting them go and she then kills him. The adult survivor then complains that what she did was reckless.
Chapter 2
Samus touches down on the GFMC Compound to find that Squad Bravo was entirely annihilated by Splinters, which she finds, questioning how such small creatures could wipe out an entire platoon. To answer her question, she watches the last recorded logs of the troops, recorded three hours prior (while ingame it was 30 days prior), with only four survivors remaining (ingame, there are none), and sees mentions of a "black fog". Samus believes they may still be alive and sets out to search for them.
Hearing gunfire, Samus finds a Federation Marine attempting to repel an Alpha Splinter, which she kill for him. The Marine urges her to kill it before the "Black Fog" comes, but she is too late. The Splinter comes back to life, now a dark color and much more powerful. While ordering the Marine to flee, Samus finds that her weapons are useless against it. She then deduces that the Black Fog strengthens enemies it possesses, and so she decides to switch to full power as well, by using her Charge Beam.
After its death, Samus wonders what world she is on. The Marine and the rest of the survivors appear, with another Marine welcoming Samus to "hell".
Chapter 3
Samus hears the stories of the survivors one by one. Klaus Schneider, the Marine Samus saved from the Dark Alpha Splinter, claims that he commanded properly, and attempts to deny his cowardness. Miguel Luis Garcia, the other Marine, seems to contain a lot of pride, and states that he "has to protect himself." Lily Thran, the woman, claims to have fainted at the time of the attack, and has nothing to say about the black fog. Jeff McCloud, the boy, says that the comm link to the Galactic Federation was destroyed, and that he cannot repair it as it is "not his specialty".
The survivors then decide they need to restore power, but Samus starts to leave. Miguel states that there is a rumor she has no emotion. Samus then states she is going to the Generator Room. All the survivors but Klaus follow after Samus, with Miguel stating that he can live longer with Samus than he can with them. The paranoid Klaus panics when he sees a Splinter corpse, and Jeff complains that Samus was moving faster. Just as the foursome arrive at the Generator Room, Klaus begins to have some hope, until they find several Marine corpses with no visible wounds.
When Lily reports that she has found a pulse on one of them, the troopers begin to wake up. Now possessed by the black fog, Samus shoots one. Ignoring criticism from Klaus, Samus continues to battle them until none are left. Klaus then believes the rumor is true, that Samus is emotionless. While still in denial over how they could have all been saved, Lily analyzes the troopers and comes up with the conclusion that once they were possessed, they could not come back. Miguel then believes Samus at least showed them mercy.
Suddenly, power is restored by Jeff. Lily, although amused because "Glasses Boy" didn't think he could do it, is snapped out of her amusement when she thinks she heard the wall vibrate. Samus' order to not touch it is ignored, and the wall crumbles, revealing a dimensional rift. Samus then orders the survivors to leave, and all except Lily do. Pleading with Samus not to leave her there, the black fog suddenly arrives, and attempts to possess Lily before Samus sacrifices herself by pushing Lily out of the way and allowing the black fog to push her back into the dimensional rift.
Samus then arrives in a parallel dimension, specifically, an exact copy of the Generator Room, but filled with poisonous gas. While attempting to escape, she notices a dark being above her that resembles her Varia Suit. Samus is last seen asking Dark Samus "who the hell are you?".