There's theories about everything from the Traveler being an ancient evil to the cryptarch being in league with the Cabal. What's a plot twist you would like to see in Destiny? Mine is: The reason we never knew anything about the Darkness is because it was jamming us. In the Great Battle for Humanity millennia ago? The Darkness invaded the Traveler and corrupted it, but couldn't destroy it. So it just stayed in there. The way we actually defeat it? Go into the Traveler itself after piecing clues together on all the planets and force an encounter with the Darkness mass control cluster. At the end? The Traveler awakens and is not an ally after all. It's been Vex tech all along. We just awoke Atheon's overseer grandfather, but unlike Atheon? He's a kind guardian who will protect humanity. Reason? We are the biological seeds of the Vex. Congrats guardians. You've been killing ancient humans all along.
What if the fallen are actually good guys but believe we and vex are darkness so the fallen and us team up to slay the vex