Fleet Admiral Castor Dane, the commander of the Galactic Federation flagship GFS Olympus, calls for a meeting with Samus Aran and three other bounty hunters—Rundas, Ghor, and Gandrayda. The bounty hunters receive orders to clear a virus from several organic supercomputers called "Aurora Units", located throughout the galaxy. The meeting ends abruptly when Space Pirates attack the Federation fleet. Samus and the other bounty hunters are deployed to the planet Norion, where the Space Pirates are concentrating an attack on the main Federation base. While suppressing the attack, Samus learns that a Phazon meteoroid, called a Leviathan Seed, will soon collide into Norion. Samus and the other bounty hunters attempt to activate the base's defense systems, when they are suddenly attacked by Dark Samus and knocked out by a Phazon Beam. With the other bounty hunters unconscious, a severely wounded Samus manages to activate the system just in time to destroy the Leviathan Seed before falling into a coma.
Throughout her mission, which eventually takes her to the Space Pirate homeworld, Samus slowly becomes further corrupted by Phazon. She manages to stop the Space Pirate assault with the assistance of the Federation troops. After stealing a Leviathan battleship, Samus and the Federation fleet use it to create a wormhole that leads to the planet Phaaze, the origin of all Phazon. Samus travels to the planet's core, where she finally defeats Dark Samus and then the corrupted Aurora Unit 313. As a result, Dark Samus is obliterated, and Phaaze explodes, possibly rendering all Phazon in the galaxy inert. The Federation fleet escapes Phaaze's destruction, but loses contact with Samus in the process. Samus eventually appears in her gunship, and reports that the mission is accomplished before flying off into space.
Samus returns to Elysia, where she mourns the loss of her fellow bounty hunters. If the player completes the game with all of the items obtained, Samus is seen flying into hyperspace, with Sylux's spaceship following her.
The director, Mark Pacini, said that Retro's biggest concern was the controls, which had "too many functions for the amount of buttons". Pacini also said the Wii Zapper, a gun shell peripheral, was never considered because it was unveiled when the development was almost done. The Retro president, Michael Kelbaugh, said the delays gave them more time to tune the controller, which took a year. He also said that while he felt Retro did "a great job" on the Echoes multiplayer, they focused on the single-player for Corruption, which they considered the franchise's core strength. The art director, Todd Keller, said the graphics team focused on texture detail and variety, making every room unique. Nintendo EAD suggested Retro turn Hypermode into the core of the game, saying it would enhance the tension as it made players powerful but leads to a game over if used excessively. Retro initially felt it would be too difficult to implement the feature without dampening the entertainment value, but after discussion turned Hypermode into a regular functionality.
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Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Phazon Enhancement Device - GF DF PX013: The Phazon Enhancement Device is based on captured Space Pirate technology. It is being tested by a GF Marine battalion based in the Norion system. Marines can initiate an energy siphon from the supplied Phazon carried in a backpack into their armorsuits. This allows them to temporarily enhance the exoskeletal and weapon systems of their armorsuits. To date, no Marines have displayed signs of Phazon Sickness, common in subjects who use the Space Pirate's version of the system. /wiki/Retro_Studios
Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Logbook – "Our Mission": Phazon was discovered two stellar years ago, and since that moment, Command has been driven to control it all. Two operations have been established, at tremendous cost. Both have failed, thanks to the accursed Hunter, Samus Aran. Her Federation allies now move to secure what little Phazon remains on the planet Aether. /wiki/Retro_Studios
Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Logbook – "First Disciples": Our struggles have ended. She has shown us the error of our ways. The way is now clear. All previous vows of fealty have been forsworn: we now pledge sole allegiance to our liberator, the great one, Dark Samus. /wiki/Retro_Studios
Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Logbook – "The Leviathan": Our leader provided us with great wisdom on many subjects, including the improvement of our mighty battleship, Colossus. We followed her teachings, and turned our vessel into a ship without peer. /wiki/Retro_Studios
Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Logbook – "Vanguard": Three worlds will be attacked, each important to the Federation. We shall destroy the spy base at Elysia, the fuel production of Bryyo, and the naval station at Norion. Each of those wretched worlds will become as Phaaze…each a foothold into the territory of the hated Federation. /wiki/Retro_Studios
Retro Studios (August 27, 2007). Metroid Prime 3: Corruption (Wii). Nintendo. Logbook – "Vanguard": Three worlds will be attacked, each important to the Federation. We shall destroy the spy base at Elysia, the fuel production of Bryyo, and the naval station at Norion. Each of those wretched worlds will become as Phaaze…each a foothold into the territory of the hated Federation. /wiki/Retro_Studios
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Tanabe, Kensuke; Tabata, Risa. メトロイドプライム3 コラプション. Iwata Asks (Transcript) (in Japanese). Interviewed by Satoru Iwata. Kyoto, Japan: Nintendo. p. 5. Archived from the original on June 28, 2011. Retrieved August 18, 2012. 田邊: それで思い出したんですが難易度の選択というのもありますよね。 アメリカ版では、時間の関係もあって、基本的に自分で選べるようにしたのですが、日本版では、任天堂らしい味付けをしようと、銀河連邦からのアンケートに答えるような仕組みにしました。 連邦のアンケートに答えるって言うのは、レトロスタジオのアイディアなんですが・・・その質問に答えると、「あなたのオススメの難易度はこれです」と教えてくれるようになっています。 メトロイドプライム3 コラプション
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