The Queen says "To the Guardians, offer the riches of our realm as bounty for these traitors."
So, now we're bounty hunters and we have nothing to do with... whatever the main story is. It's not even like we're saving the world(s) from an invading force. In fact, it looks like The Fallen are fighting for their own independence, and we're being hired to push them back into slavery. Remember the first time you visit the Queen, and she has the Fallen under mind control?
Wait, are we the bad guys? Hired muscle, hunting down refugees in search of a home and peace, in exchange for glimmer and guns? How far have we fallen since we first woke up in that junkyard?
Or is it like one of those - Han Solo in Star Wars - kinda things where we're just wandering bounty hunters doing our own thing when all of a sudden we walk into an ancient prophecy, blah blah blah, save the galaxy.
Actually, it would be kind of cool to be a bad guy for a change...
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The Fallen may be running from the Darkness, but they don't act like refugees. They act like pirates, and now it seems that they act like bandits. We Guardians aren't bandits. We aren't pirates. We are privateers. We are mercenaries. We fight for our factions, we fight for the Vanguard, we fight for humanity, we fight for loot and upgrades. We fight for pay and the right to exist (because sometimes you can stand up for your ethics and get paid) The Awoken are our allies, for some of us they are our ancestors. We came to them in a time of need and despite acting like dicks, they did help us. Now they want our help, and they want to pay us? We'll be there. So no, we aren't the bad guys, though we're definitely not 100% moral good guys looking for a diplomatic solution to every problem, but then who expects us to negotiate with Hive or Vex? Only the Fallen seem even slightly open to negotiation, and they renege on those deals!