So? It doesn't make sense that we killed Atheon over a year ago and I went down to the vault last night and the cheeky little twot was still down there.
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In the style Destiny is, he's there because in this game you need to grind your ass off every boss. The difference now that should make them not playable now is that the game has pointed out in game that we have defeated them (See mission Paradox).
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Vault of Glass with taken enemies sounds okay, lore wise. Maybe there could be a kind of restorative mind for Atheon or the Templar?