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.
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Stranger works for nine, cabal are the alien force that made a pact with the nine for their own survival, stranger watches us and tells the nine what we are doing, xur comes and sells weapons and armor to prepare us for the taken, the cabal fall to the taken, we help the nine and defeat oryx