The captain of the starship went by the name Jahveh. A mutiny took place on board. A high ranking officer by the name of Lucifer and his followers were exciled to earth after the failed mutiny. The unexplainable alien technologies were viewed as miracles by the primitive human civilization at the time. The starship stayed with humanity for a long time until the captain's son was crucified by the people on earth. The aliens gave up on humanity and departed, they promised to return.
Those atheists believe the books of Bible can be consistently explained in terms of alien visitation. The sharp difference between the angry God who flooded and burned humanity in the Old Testament and the lack of similar punishments in the New Testament and in today's world was explained by the departure of the starship.