After Samus left Phazons core, Dark Samus awoke and made her escape on a Leviathan, she made a random warp to a peaceful looking planet, and planned to convert it into a new Phaze!
(This is the start of a long series of crossovers, all of them taking place in the same time line, This story was inspired by Metroid: Equis, I recommend you read it, and if the author us reading this (sorry I forgot your name) tell me what you think)