Operation Phaaze is a mission based on the events of Metroid Prime 3: Corruption detailed in the KhaosOmega-written Amethyst Angel Adventures story of the same title. Notable differences include Samus (there being two of her) and the other three Hunters not being infused with Phazon during the attempt to prevent a Leviathan impact on Norion, thanks to Phazon-manipulating Nikki Stewart interfering with Dark Samus, the aforementioned dual Samus variants along with four XQ-linked characters, weapons not in Metroid Prime 3, and two Khaos-created Power Suit variants, from the 'XF Series', which two of the four others acquire during the mission. Also notable about Operation Phaaze is that it follows the other Prime Trilogy games in being a KhaosOmega-written fanfiction based on a Metroid Prime Trilogy game, after 'Relics of Tallon IV' (Metroid Prime) and 'Echoes of Aether' (Metroid Prime 2: Echoes).
Operation Phaaze takes place somewhere in KTS Year 2012, when four XQ agents (Nikki Stewart, the Phazon Warrior (for her unique ability to absorb Phazon harmlessly) and the ZK3 trio, which includes the AAA series' titular codenamed character) and a second Samus Aran appear in the GD dimension system through two separate rift portals (different from those used to traverse between Light and Dark Aether) and proceed to a Galactic Federation vessel to defend it from a Space Pirate attack. The combined firepower of five hunters makes taking out the Space Pirates easier. Afterwards the five, plus the three other hunters from Metroid Prime 3, head to Norion as Space Pirates are attacking the planet. Somewhere along the way a fight against Meta Ridley occurs, and then a Leviathan is sighted approaching Norion. When Dark Samus appears to incapacitate the hunters and ensure the Leviathan impact Nikki immediately unleashes her Phazon powers to incapacitate the Phazon clone of Samus instead, allowing Anise to use the XQ-designed Chrono Eclipse Cannon to destroy the Leviathan before impact. Following the Norion incident the six head to Bryyo, where Rundas uses his cryokinesis to assist the group. Once the group reaches the Leviathan core Nikki unleashes her Phazon absorption ability again to free Bryyo from Phazon corruption. Elysia and Urtraghus, the Space Pirate homeworld, are also spared from total Phazon corruption, as Tallon IV and Aether had been prior to Operation Phaaze. It's on Urtraghus, though, when an XF Series Power Suit model is equipped by Metroid Squad Agent Iota upon acquiring the Nova Beam, a model dubbed the Zonova Suit for its crystal coloration and special Amazonite Beam (another Khaos creation). Anise, who would later join the Metroid Squad herself as Agent Psi (as Jet Brazie, XQ Captain and Anise's 'secret crush' at the time she joined the Squad, was Agent Omega), would later obtain her own XF Series model, the Ice Star-based new Zonova Chill, one of three models combining the Zonova's special beam with a 'Raiden Trio' model's signature Grapple Beam-side elemental weapon (and, in Anise's ice-affinity case, the ability to kill Metroids on contact as long as they weren't a Fission Metroid having undergone its namesake fission and colored to a weakness other than ice); the Zonova Fusions give females not blonde like Anise, a redhead, access to their Zonova side's exclusive weaponry but boosted by their Raiden Trio side's own signature weapons and partial 'Contact Kills Metroids' bonus. Their downside is that those capable of acquiring a Zonova Fusion have to accompany a blonde on a Metroid Prime 3-based mission and resist the temptation of gaining a Raiden Trio model until the blonde gets the Zonova Suit upon acquiring the Nova Beam on Urtraghus.
In the end, the six-hunter platoon locates Phaaze and, once close enough, Nikki activates the Absorber Vortex trick one last time, but this time enough of a charge is present to fully absorb all of Phaaze (with help from numerous energy attacks from ZK3) and forces the stolen and corrupted Aurora Unit 313 out for a one-shot kill via the Chrono Eclipse Cannon wielded by Anise. Dark Samus isn't as lucky, as her Phazon composition results in her being turned into pure Phazon accessible for use by Nikki at a later date.
There are ten notable individual characters in this KhaosOmega fanfiction.
- Samus Aran (GD system): the local dimension system's variant of the Metroid series' signature character. It is through counterpart connection that her GX variant (and by extension ZK3 from the GX variant and Agent Iota having been through the mission before, hence their leader roles) arrived in her native dimension system.
- Samus Aran (GX system): Metroid Squad leader (codename unknown), using her experience of the mission to act as co-leader of the squad alongside the other mission-experienced hunter, Metroid Squad Agent Iota. That experience also allows the small six-hunter platoon to handle certain enemies easier than Samus alone in the game.
- Rundas: a Phrygisian hunter who assisted the small platoon during the Bryyo portions of Operation Phaaze. Spared from corruption due to Phazon self-production by Nikki.
- Ghor: unknown species from Wotan VII, who assisted the small platoon during Operation Phaaze's Elysia portions. Spared from Phazon corruption by Nikki.
- Gandraya: unknown species, possibly from Jovia XII, assisted the small platoon during the Urtraghus portions of Operation Phaaze. Was not corrupted by Phazon thanks to Nikki.
- Nikki Stewart: A GX native, XQ agent 59 and their Phazon Warrior, possessing a unique power to absorb Phazon with no ill effects, then use it for devastating results against enemies. Uses her Phazon powers to mess with Dark Samus on Norion, then absorb the entirety of three Leviathans as well as the entirety of Planet Phaaze (killing Dark Samus and expelling the corrupted AU313 for Anise to kill)
- Dark Samus: born of Phazon and the remains of Metroid Prime with some of Samus's DNA and her Phazon Suit, the main antagonist like in the game. Unable to corrupt the hunters on Norion due to Nikki interfering, then killed when Nikki's Phazon absorption power converted her into Phazon
- ZK3: a trio of XQ agents (Peach Rochelle Gordon, Metroid Squad Agent Iota (29M, native to GX); Dawn Brayzii, cousin of Metroid Squad Agents Sigma (Katey), Tau (Hollie), and Omega (Jet) (74P, native to GX); and Anise Azeat, the AAA series' titular codenamed character (07GZ, OZ system native)) on the mission. Rochelle's experience of the mission makes her a co-leader, eventually acquiring a Zonova Suit on Urtraghus (which triggers Anise later gaining her Zonova Chill model). The trio is also skilled at energy attacks (Anise using her self-created Chrono moves, which have numerous wine red streaks through them) and special powers. The Leviathan headed for Norion and Aurora Unit 313 were both instantly destroyed by contact with the beam from Anise's uber-strong Chrono Eclipse Cannon.