Warning possible spoilers ahead but basicly
Atheon is the good guy who isn't realy trying to write the Vex into the universe, but trying to stop the rise of the Darkness
[spoiler]Atheon is really Martin O Donnell who's musical exelencce ascended him into a higher plain of existence. His amazing music has become so perfect that it created the Vault of Glass which maniplulates reality itself and the Vex. Contrary to the belief of the Tower's inhabitants Atheon's goal is not to controll the Universe but to rewrite a major mistake that doomed history forever.
The mistake that created the Darkness, ended the golden age... that mistake is letting Bungie side with Activision.
[/spoiler]