Personally I'm not sure if the queen is actually dead. I mean, in the opening cutscene, we see that the queen's powers can extend far beyond mere ruling. Maybe she found a way to escape using her literal space magic? I dunno...
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She's alive. Her brother, dead. She's going to go down a dark path and blame the guardians. She was helping us & it got many killed. We may have to defend from the Awoken. *All a theory. But games have done things like this how many times now?*