So we are dead, but not dead... Undead in fact...
WE ARE ALL ZOMBIES... MWAAAARRRRRGGGGHHHH.
Seriously though... I hope they explain how we came to be more when the game actually ships. If you were woken up by a Ghost and told "You've been dead for for a... long time!" you would freak out.
DNA scan... matter transmuted into living flesh and then the ghost... implants a soul maybe? Perhaps that is why your Guardian takes it all in their stride. They are pre-programmed to not question their resurrection. If it was me I would be going "WTF HAPPENED... I leave for five minutes and the universe goes to hell in a handbasket. AND WHO WRECKED MY CAR???"
One side note... We have Guardians in Destiny and the next Halo is called... Guardians. WHYWHYWHY? I can just imagine going out in the solar system in Destiny and coming across.... Guardian Chief (he got promoted) and Cortana (who is now an Awoken). That's another thing... why are Bungie into blue babes (ie the Queen of the Reef this time)?
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Wtf did all this armor come from?