How to beat the six-eyed beam-monsters
While in energy form, shoot each of the six eyes so that they are all open at once. The monster will then spin, likely spraying you with a few waves of laser fire. Then you will see a brain-like structure grow out of the creature's bottom. This spot is vulnerable; shoot it repeatedly to win.
You will need to do this three times to access the Cathedral basement.
How to kill Mithala
In the Cathedral basement you fight Mithala, the god of the Mithalans. You kill him by putting mutants that he spawns in the gas at the bottom and then feeding them to him. After feeding him three he will tear out his eyes. Then you use shield to bounce his huge fire balls back at him. That kills him. When he is dead you get a vision about the destruction of Mithalas.
Note: Energy will make him step back but won't damage him.