Remember when we got Ruinous Effigy? A weapon made by the darkness in a place of light. Used by us protectors against our enemies. What if the Darkness is being controlled by the Witness. In my opinion, the Witness is the main antagonist of the story and is corrupt by power in a way to bring everyone to "Salvation". I for one believe so, since they can control the Black Fleet and speak through the darkness. Because I remember Savathún talking about the Witness being a Mortal before becoming this God like Entity. What if they have a deep connection to the darkness that overthrows the own mind of the deep itself. The Witness also seems eager to get to the Traveler as well, as if to use it instead of destroy it, maybe that's what will happen in Lightfall