The Leviathon Seed appears in Metroid Prime 3: Corruption and also was the basis for Metroid Prime and Metroid Prime 2: Echoes. The Leviathon Seed comes from a very far away planet called Phaaze, and they hurtle through the universe and strike planets, thus corrupting them with Phazon.

The first one known hit Tallon IV, causing the Chozo to die out and corrupt the planet with Phazon. The second known one hit Aether, and considering Aether had an already unstable atmosphere, the strike of the seed created a darker dimension of Aether called Dark Aether. Even the Luminoth in Metroid Prime 2: Echoes say that Dark Aether came only after a 'meteor struck'.

Dark Samus and the Space Pirates took over Phaaze, being able to send out leviathon seeds at will. In the end of Phaaze saga, the Galactic Federation used the powers of a leviathon seed in the Pirate Homeworld's orbit to open a wormhole that would lead them to Phaaze. After Dark Samus' defeat, Phaaze exploded, ridding the universe of the Phazon threat forever.