Metroid Prime 3: Corruption
It turned out that Phazze, a planet, was the source of Dark Samus, as well as the source of all Phazon. It would send meteors called "Leviathan Seeds" to some planets, like it did to Tallon IV and Aether, splitting Aether into Light Aether and Dark Aether. It is made of pure Phazon, with gaseous Phazon for its atmosphere, liquid for its "water", and solid for its ground. With its destruction, all the Phazon in the universe is destroyed, even the Phazon in Samus herself.