In Xenogears, a PS2 game from several years back, you spend the entire game trying to stop this evil genius from reactivating an "ancient" weapon that will destroy the world. There are several Biblical references but the game takes great pains to assure you are just there because the creator liked the names (Adam and Eve were two slaves who escaped a tyrant to find a new nation, Cain and Able are two waring kings, etc.). The game also goes out of its way to assure you that this is NOT earth.
Then, you come to the final battle. The Baddie has activated the ancient weapon, called Deus, but one of the characters, whose life-energy is being used the power the thing, is able to force Deus out of the planet's atmosphere. The hero hopes in his battle-mech and flies after Deus, gets eatten by Deus, and fights the evil genius to rescue his girl. Though the Baddie's mech is destroy, it is revealed that you cannot kill him because ...
He's a member of the Heavenly Host who was banished millenia ago. The only way he can get home is to destroy Deus, a machine in which another one of his kind was trapped by Earthian humans hoping to use her as a weapon, which will rip reality open and create a portal to heaven. He explains that humanity ended up on the planet when the captured angel refused to co-opperate with the Earthian military, so they put her on a ship with the intension of shouting her and the Deus, which had developed into a sentient being, into a black-hole. Deus revolted, which caused the ship to crash and the angel imprisioned Deus in the earth, took on human form and gave birth to a new race of humans using the DNA of the dead humans from the ship.
So, Deus starts to implode, a portal to heaven opens, the Baddie spreads his wings and flys away as our the two humans race back to the hero's mech. As the portal closes and the angels go home, our hero and his girl return back to the planet in the giant mech that has sprouts angel wings as a sign that they are loved by the Heavenly Host.
After the credits were finished rolling, I dropped my controller and shouted "WHAT?!?"