Games where the plot revolves around a corrupt religion etc

Xenogears, Xenogears, Xenogears. Not only does it fit the criteria you described but it is also one of the most amazing RPG's to ever grace the planet. Xenogears is my all time favorite video game. One would be hard pressed to find an equally complex and engaging story as Xenogears, even in modern books and movies. Play. This. Game.

I'd seriously suggest stomaching the use of swap magic on this one. It's just that good.

Jam it back in, in the dark.

Originally Posted by Enkidu

the whole Billy thing and that Father Stone was only a minor point if you look at the entire plot, you can't really say that the game is about a corrupted religion because of that. It uses a lot of religious terms, and the whole "god" thing, but this alone does not qualify the game as having a corrupt religion.

I stand corrected. I still, however, would suggest Xenogears because it's an amazing RPG in it's own right. If the original poster has not played it and is a fan of RPG's then I strongly recommend it. Trying to summarize the plot in Xenogears is rather difficult. I suppose if you wanted to summarize the entire plot you could say that it's a story about man fighting and destroying his creator. This hardly suffices though because there's so much more involved than that.

There's nowhere I can't reach.