Savathun created an illusion to trick the Witness. Most likely, the illusion was the traveler being destroyed, which would explain why the Witness returned to dark space because he would have had no purpose. Meanwhile Savathun also used random humans to cast a hive spell to trap the traveler on earth and Savathun killed Nezarec as well as helped to conceal the veil.
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That would of worked until Bungie said he has the Vex make the Black Heart. Because that shows it knew the truth. They tried tying off too many loose ends and wound up making knots.