Samus Aran in the new PED suit.
- - - Mission File 02904 - - -
The ING have been defeated, as has Dark Samus. Samus Aran soon gets another notice from the Federation. This time she and three other hunters, Rundus, Gandrayda, and Ghor, must purge a Phazon-virus from the Aurora Units and get the Federation network back online.

After the briefing, the GFS Olympus is attacked by Pirates. When Samus and the others arrive at the planet Norion, they find a large, Phazon-filled seed known, as the Leviathan is about to impact the planet. After destroying the Seed by means of Norions defenses the Hunters are attacked and corrupted with Phazon by Dark Samus.

When all the Hunters awake a month later it is observed they can now produce Phazon from inside their bodies. Armed with this new power the Hunters are assigned to purge other Aurora Units of the Phazon. On the planet Bryyo, Rundus was discovered to have been corrupted by the Phazon completely. After getting Bryyo’s AU back online Samus heads to Elysia, where it is found Ghor has also been corrupted. After getting the AU back online on Elysia, Samus finds Gandrayda corrupted on the Pirate Homeworld. After getting all AU’s functioning properly again, Samus gains control of a Leviathan, making it open a wormhole to the planet Phaaze, where Dark Samus and the Space Pirates obtain Phazon.
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