After all the Anu on the planet surface were wiped out, the ones up on the ship and the moonbase continued to fight with each other for power. Their struggles got increasingly violent, and the ones with the greater advantage were those who were most savage and eager to control.
Eventually, there were only two left: Ishtar and her follower Yahweh. Ishtar and Yahweh had worked together to gather all the power, and destroyed or enslaved the few of their kind who remained.
They replaced the other Gods in the mythologies of the humans. Locals were told their old Gods had lost, or were evil and should not be followed. In some cases, Yahweh and Ishtar simply took over the communications channels. Between them, they controlled humanity.