Ye shall be as gods is a recurrent theme seen throughout Xenosaga and Xenogears.
Origins[]
It originates from the story of Genesis 3:5 of the Bible. In it, a serpent offered Eve a fruit and told her that if she ate it, humanity would become "like gods".
Xenogears[]
It is used in the introduction of the game. When Deus takes over the Eldridge, the repeated text "You shall be as gods" covers their monitors.
Xenosaga Episode I: Der Wille zur Macht[]
"Ye shall be as gods" is KOS-MOS' log-in password. In the beginning of Episode I, Shion types this into connection system NATARAJA before entering the Encephalon to run tests with KOS-MOS.
This is called back to later when Shion Uzuki finds KOS-MOS in her Encephalon subconscious domain, which is Rennes-le-Château. KOS-MOS is found bound with red and blue wires to a cross, with her arms splayed out as if she was being crucified. Shion makes the sign of the cross over KOS-MOS and chants "Ye shall be as gods".