Final Fantasy X was produced by Square Enix as the flagship game for Sony's new Playstation 2, about ten years ago. The game, like all JRPG games, was primarily intended for a Japanese audience, but the plot of the game struck hard with a lot of Catholics, especially ex-Catholics, in the Western world as well.
Like all Final Fantasy games, the core premise was of a rag tag group of fighters with various abilities fighting against an evil monster that was trying to destroy the world. Unlike a lot of the previous games, the "evil monster" of X contained a bounty of religious overtones. (If you want some fun anti-corporatist overtones, play FF7, where the evil monster is actually the Shinra Corporation.)
Your main antagonist was a giant sea monster called Sin. Your "not quite sure if ally or foe" was a slimey priest named Seymour, recently named to a very high position within the Church of Bevelle. The religion in question was the Followers of Yevin, Yevin being a prophet that spoke out against the evils of technology during a war that nearly destroyed all of civilization on the fantasy planet Spira a thousand years ago.
There are a lot of parallels to the fall of Rome, and the subsequent rise of the Church to fill that particular power vacuum in the ruins of civilization.
The game begins at the End of the World:
Things are, of course, not as they seem. The people of present day Spira are taught that Yevin was a benevolent prophet, and if they follow the teachings of Yu Yevin they will be saved from Sin.
Sin, as I mentioned, is a giant sea monster. He appears and reappears pretty regularly. (The linked video is the first appearance of Sin, whereupon he destroyed the city of Zanarkand first.) Spaces in between when Sin appears are referred to as "the Calm." A calm could last ten years, or fifty years, but Sin always comes back...
The only people capable of defeating Sin are the summoners, who must go on a pilgrimage to temples across the world to collect their aeons, spirits of priests and priestesses from the past who agreed to be frozen bodily to allow their souls to gain more power. They are the saints of this world - and by allowing their soils to be trapped, they have become incredibly powerful.
Once a summoner has obtained all the summons, his or her last journey is to the ruins of Zanarkand (Rome), where she obtains the final Aeon. Yunalesca, the saint who is the daughter of Yu Yevin and the first High summoner to defeat Sin, will grant you the final summon in exchange for your life and the life of one of your comrades.
The High Summoner dies. The Final Aeon, the sainted form of one of her comrades, obtains all the power necessary to defeat Sin.... but Sin returns.
Your particular party is not too keen on this turn of events - why should two people have to die? Your summoner was prepared to sacrifice herself, but not her beloved friends. So they go down in a blaze of glory and defeat Yunalesca... and then the story unravels.
Heaven is called the Farplane. Souls that are unable to travel to the Farplane, if they are not Aeons, become monsters. Humans whose souls still inhabit their bodies are called the Unsent.
As you return back to the Church of Bevelle, you discover that the entire church is run by Unsent - they are set in their ways because they are zombies. Some of the church leaders date back a thousand years to the war on Zanarkand.
Sin was first summoned by Yu Yevon himself as the weapon of choice against Bevelle. His "teachings" explain that technology is bad and Sin attacked Zanarkand first because it was the most technologically advanced city, but in reality Yu Yevon has been ruling the planet and the Church of Bevelle with an iron fist ever since Zanarkand was destroyed, as he formed a treaty with Bevelle to prevent the city from being destroyed. He has been sacrificing summoners and their friends ever since in an eternal summoning, using Sin's power to keep himself alive. The Eternal Summoning is also used to power a dream version of Zanarkand that exists in perpetuity; the Aeons all summon it together in a fond memory of their home. The Church of Bevelle, filled with Unsent zombies, exists solely to protect Yu Yevin and keep the population at the mercy of Sin.
And it's up to your party of ragtag adventurers to stop this.
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The developers at SE have denied that the game is an attack on the Catholic church. They actually intended it to be more of an argument against some of the mistakes of the Shinto and Buddhist religions in the past, and consider the game to be steeped firmly in Japanese history.
Not all of us buy it.
Whatever the inspiration was, Final Fantasy X presents a powerful argument against letting a central church dictate to you how to live your lives. The one tribe of people who continued to build and operate machinery, the Al Bhed, are considered outcasts by the Church. Everyone else has gone from an age of technological wonder and magic to a miserable feudal system where your entire village can be wiped out by a tsunami from Sin at any moment.
If you have a Playstation 2 I strongly encourage you to give Final Fantasy X a play through. It actually lends itself to people who don't normally enjoy video games, as the battle system is "conditional turn based" (more like a chess game) which gives you time to think about your moves, or drop the controller and go take care of a crying baby or hungry husband without worrying about dying mid-battle. (Another excellent game that uses this system is Final Fantasy Tactics.)
And if you're an ex-Catholic like me, you'll take a particular bit of pleasure in destroying the church of Yu Yevin, bit by bit, to free the people of Spira from Sin once and for all.
Edit: Corrected my factions. Even having played through the game twice, it can be a bit confusing!