This is how you kill Atheon. (Destiny)
So I was running the Vault today, we had Atheon's health about 3/4 of the way down in the third teleporting sequence, I screwed up my ground pound and the accursed health-regenerating Minotaur killed me. My teammates grabbed the Relic, but alas, it was too late. As we waited for the inevitable restart, this happened.
Atheon apparently decided he didn't feel like living anymore.
I think he actually suffered from severe depression.

Was No One In The Vault Area?
No one was able to see what happened? That's weird.
I wonder why that never happened to us the 35+ times we died in that Rookie Raid...
Nope.
Not a single person in the Vault and I doubt they could've killed him in that amount of time had anyone actually been in it, seeing as Time's Vengeance wasn't active. Nobody had any idea what happened. But I'll take it!

Answer
You are supposed to leave the Vault behind and run the Crota raid instead. The Bungie Gorgons erased Atheon from existence. Go play the new raid they say!

Oooooooooooooook........
Dafuq?
You're a wizard.
But I need some shards to upgrade my new armor to get to level 31 before I do the Raid. Haha.