The golden rule of any narrative states that a protagonist is a good guy, so it is a common sense to believe that when you play as a protagonist in the game, such as the Guardian in Destiny, then you are a good guy.
But what if it’s not true at all? What if Guardians are just as bad as the aliens that they fight against? The hints to this can be found while you try to sneak up to Fallen Dregs, who will notice you and yell: “It’s the Darkness!” As you may know, the Darkness is the destructive force in the universe of Destiny, so why would they call us the Darkness? That’s a really good question, isn’t it?
On top of that, ask yourself: why the enemies are called Wizards, Knights, Acolytes, but your team is called either Titans, Hunters, or Warlocks, which all have evil connotations to them. Or how about the titles of the quests you are given, such as Slaughter the Fallen, Kill Them All or Decimate The Hive. Why not something along the lines of Save the World or Protect the Innocent?
Anyway, there are a lot of good points in this theory and you may see yourself in the different light from now on when you play Destiny again.