....well you start off wrong so....
Atheon isn't a prisoner.
Now that I have a moment let me explain a little bit.
The Vault of Glass is how the Vex want the universe to be, a construct where they have ultimate power. It's unknown if Atheon created the Vault or if the Vault created Atheon, but it's because of this that i believe this is a temporal causality loop. Essentially... the Vault was created by Atheon so that the Vault could create Atheon to create the Vault so that.... (this goes on infinitely)
While I'm here, no Atheon's not against the Black Heart. The Garden was actually the Vex's attempt to further the power of the Vault into all reality. Yes i know "but his name!" Yea yea that means something more interesting actually.
Atheon is derived of atheist, and eon, it's not that he doesn't believe in the Black Heart. He doesn't believe in time.
English
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I always thought the heart was a tiny spec of the "darkness".
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How did you arrive at the concept that Atheon is against time? Sounds very interesting
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He may not believe in Hive gods either... Like Oryx.
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Well i mean....you can't not believe in a physical thing. It's there
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Not the thing, the concept. The Vex are beings of logic, aka no space magic. Quria was the Vex mind that first met Oryx. He tried every method of logic to kill oryx, but he couldn't. Oryx got his powers from faith and sacrifice with his sword logic. According to the Vex, that makes no sense. So, the vault of glass is made as a simulation of oryx's throne world, but with logic at it's center rather than faith. Thus, the boss, atheon, is the direct manifestation of logic, which means that he can not believe in any sort of god in general since that would defy the logic the Vex spent endless timelines proving to be the true power in the universe.