I'm a student of religion and I'm a gamer. I've seen religion used as a plot device in a few different ways in games, but I can't help feel that it's always a tired cliche rather than a vibrant element to the story. Religion is still an important feature in the lives of most people on the planet, and for the sake of fiction it adds flavour and depth to a character and a story.
Perhaps the most obvious use of religion is the religion as institution. When you're thinking about how to establish a religious institution in your game, you need to acknowledge that it is an institution in society, for better or worse, like all other institutions. It's a socially-acknowledged organisation with legal status, authority, responsibility, symbols, finances, people, buildings, rituals and goals. The religious institution almost certainly has political aspirations, preferring one kind of government or ruler over another, whether overtly or covertly expressed. Think about who the secular powers are in your game and decide whether the established religion supports them or not. Are they working to undermine the ruler or to strengthen the dominion? Perhaps they are trying to subvert an unjust king without being discovered.
As an institution, the inner workings are hidden from the view of outsiders. Consider the tax department as a secular parallel to get my point. And where things can be hidden, someone will find a way to hide their evils in amongst it all. *cough* *Enron* *cough* Contemporary examples of this in Christian institutions include pedophilia, embezzlement, adultery, and so on. In short, everything that the religion opposes has probably been hidden in the institution. Which evils are hiding in the institution in your game? Who is hiding them? Who is committing them? In this way, the religious institution is no different to a corporation or government department, and it makes for lots of plot opportunities.
Also, an institution is something that people can't disbelieve in. It's there, and is an agent in the society. Regular people will interact with it somehow, perhaps through temple attendances or street parades. They almost certainly will touch on certain festivals or holy days, either as historical remnants or as a living and vibrant day. Holy days can be solemn, reflective, relaxing, celebratory, ecstatic or even orgiastic. Which kinds of holy days are included on the sacred calendar of the religions institution in your game? What do they celebrate?
The last thing I'll say about religious institutions in your game is the role of religion as ideological enforcers for the established order. Historically, we've seen this in Europe as the Inquisition. Today, this is the actually existing condition in Iran, as applied by the Guardian Council. In fiction, I especially like the Jedi Council as an example. The religious institution interprets the ideology and has authority to interpret and enforce it. In your game, you would need to think about the tenets of the religion, the interpretive structures of scholars and clerics, the powers (legal or supernatural) of the enforcers. Remember that they all believe they are safeguarding the One True Way. You might also need to think about what could happen if they don't safeguard the community or nation. Will the deity bring calamity because of unfaithfulness? Or is the deity a little patient?
These are just four ways - an organised entity in society, a haven for corruption, an agent in society, enforcers of ideology - for you to bring a religion as an institution into your game.
After writing this post, I find myself brimming with ideas about how other aspects of religion can contribute to your game. And that means more posts on the subject. Watch this space.