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[silently hopes he isn't being annoying]
Samus herself didn't really vaporize Dark Samus. She hurt her and then she fused with the Aurora Unit. When Samus damaged the Unit enough the planet was destroyed because of the Aurora Unit dying. Phaaze, being the source of Dark Samus, wouldn't have been able to regen her because it, well, died.
Think of it like Mother Brain. When you kill her, the planet gets destroyed, but this doesn't mean that Samus can destroy Zebes.
Also while it may just be PIS from a perspective it seems odd to me that she has Small Star durability yet feels the need to escape when a Space Pirate base is set to self-destruct.
Samus herself didn't really vaporize Dark Samus. She hurt her and then she fused with the Aurora Unit. When Samus damaged the Unit enough the planet was destroyed because of the Aurora Unit dying. Phaaze, being the source of Dark Samus, wouldn't have been able to regen her because it, well, died.
Think of it like Mother Brain. When you kill her, the planet gets destroyed, but this doesn't mean that Samus can destroy Zebes.
Also while it may just be PIS from a perspective it seems odd to me that she has Small Star durability yet feels the need to escape when a Space Pirate base is set to self-destruct.