(Spoiler Alert for: Assassin's Creed 1, 2 and Brotherhood, Final Fantasy X, XIII and Tactics, the Halo franchise, and Skyrim. As usual, you have been warned.)
I think it can be said that games are becoming more and more prominent as a valid form of speech and expression of ideas and beliefs. With that in mind, what games say regarding certain topics should reflect the dispositions of the people who both create and consume them. One particular topic springs up with a fair degree of regularity in video games, which I find quite interesting. That topic is religion. Religion is a very huge topic in modern society that permeates all of our lives, regardless of what each person thinks regarding the subject. It influences people and their opinions. That is why I find what games have to say on this topic to be worth discussing and why I have made this subject the topic of discussion.
But before I begin, I want to make one thing completely, totally, unequivocally clear. I have absolutely no problems with religion. This analysis of the subject is intended to be as unbiased and objective as I can possibly make it. I have no desire to offend anybody and I hope what follows is indicative of that. What I am going to do is look at the common themes surrounding well known takes on religion in video games and take a look at examples of them. Then I will try to look at the big picture surrounding this and put this all in context.
One of the most common themes that games touch on regarding religion is that it leads to war. Many games build major plot points around this concept. An example of this comes from the most recent game from The Elder Scrolls franchise, Skyrim. In the game, there is a Civil War tearing apart the nation of Skyrim. The central reason for this schism, at least on the surface, is that the Nordic people have been banned from publicly worshiping the god Talos, who is the ascended soul of the first emperor of the realm, by the Empire because of a recent treaty with a rival faction. The churches were all forced to disown Talos as a god and go from praising the Nine to praising the Eight. The outrage and religious fervor was so great that it lead to the birth of the Stormcloak Rebellion. This is far from the only example of this. The original Assassin's Creed was publicized beforehand as taking place during the Third Crusade and using it as a backdrop for their story, one of the more famous/infamous Holy Wars in history (depending entirely on your viewpoint), and they milk that setting for all it is worth. The characters in the game often muse on the nature of war and the people who fuel it, pondering the causes behind and reasons for it. They constantly question the necessity of the Holy War and it is really fascinating, though Ubisoft was not the first company to question the nature of crusades in a video game.
In fact, the Halo series did this well before Assassin's Creed came out. One of the major threats to humans in the Halo games is an organization of religious alien races referred to as the Covenant. This group attacks humanity because they believe that their gods have condemned humanity and wish to have them eradicated. This is one of the series central conflicts and even gamers who are not fans of the franchise (like myself) have a passing familiarity with this plot point. Even Final Fantasy gets in on the action. In the franchise's thirteenth main installment, there are two worlds, Cocoon and Pulse, that each have their own gods that preside over them. These two worlds have been at war with each other for years. As the game's main plot progresses, it is revealed that the gods themselves are orchestrating the war in order to get enough people to all die at once for the gate to the next life to be blown wide open so they can meet the deity who created everything. The gods themselves organized a war between two worlds. That sends a pretty powerful message as to the subconscious of the developers.
The other theme that tends to surround the portrayal of religion in video games is the theme of the church as a tool for political corruption. Going back to the Civil War plot line in Skyrim, the political intrigue surrounding it is relevant to this point. The founder of the Stormcloaks is revealed towards the end of the Civil War plotline (should the player choose to side with him), to not really care all too much about the Talos worship ban. It bothers him to be sure, but it is far from his main motive. All he truly cares about is political power. To that end, he stirred up a religious movement and used it in order to take over the land of Skyrim as High King. Political motivations for religious movements is also a trope which the Final Fantasy franchise is very familiar with. At least two different Final Fantasy games that I know of (Final Fantasy X and the spin-off Final Fantasy Tactics) use this trope to great effect in their stories.
In Final Fantasy X, the world of Spira is perpetually threatened by an entity referring to as Sin. According to the reigning religion, Sin was born because of humanity's reliance on machines and weaponry and that it needs to be exorcised by following precepts and praying for humanity's collective atonement. The game reveals later on that it was all a complete lie. Sin was created as a way to preserve the collective memories of a fallen city and the religion was founded in order to gain political control through false hope that it could be defeated through strict adherence to it. The other example of this trope in this franchise comes from Final Fantasy Tactics. The game revolves around the political intrigue between several noble houses, all of which practice the leading religion of the land. According to the tenants of the religion in question, the leading Saint, St. Ajora Glabados, and his 12 disciples wielded the fabled Zodiac Stones to defeat a massive evil a long time ago. The modern church officials attempt to use the Zodiac Stones to consolidate power and maintain their influence on politics. While they are shown to be corrupt, even they do not know the truth and genuinely believe the stones will provide salvation. However, as the game goes on, a horrible truth is revealed. The Zodiac Stone are conduits for the Lucavi demons to form contracts with humans. These human gain great powers, but are eventually turned into nothing more than avatars for the demons will. Saint Ajora used this long ago and merged with the demon Ultima, head of the Lucavi, and, with that power, gained Sainthood and massive influence on the people until well after his death. The protagonist of the story works behind the scenes to collect the Zodiac Stones and prevent another catastrophe from being unleashed on the world.
My final example comes from the Assassin's Creed series again, particularly the second installment and its follow up, Brotherhood. A major plot point in the these games is that the main adversaries, the Knights Templar, have taken control of the Vatican via the papacy. They use their influence from this position to assert control over the area. They bribe officials, threaten the people into compliance, warping religious texts to their advantage, and many other things. They did not make up most of this either. The people involved, Rodrigo Borgia and his family, were notoriously evil people who abused their positions in the church to better their own ends. The only thing Ubisoft made up was that they were a part of the Knights Templar. It is interesting to see a franchise comment on history the way that Assassin's Creed does. It provides food for though and conversation.
To be fair to game developers, there are also plenty of examples of religions in games displayed in a more positive light as well, but these are typically left unexplored and exist superficially and/or as a way to give players a place to get healed and buy healing items/spells. More often than not, when a game explores the concept of religion intently, it is shown in a negative light. While this would indicate that gamer culture does not think highly of religion, I honestly do not think that is true. Many of the people I know who play games are highly devout in their chosen faith. Most of them are also very kind people on top of that. So then why do games tend to be so highly critical of the concept when compared to other media? Is it because of some subconscious reason that we are only superficially aware of? Is it because the medium itself allows more a higher degree of nuance and intrigue in this topic? Is it simply because corrupt churches make for interesting plots? I honestly do not know the answer to this question. My job is simply to highlight an aspect of games and get you to think more of the subject. I am no where near intelligent or unbiased enough to give a good explanation. I leave it up to you to think and debate with yourself and others to find an explanation behind this conundrum.