Scary Amoral Religion

When you look at a Scary Amoral Religion, at first it seems to have no scruples whatsoever. The doctrine it preaches condones acts of unprecedented brutality. They stand on the brink of ending civilization as we know it, and all because their God says so.

They look like a Religion of Evil. They even act like a Religion of Evil. But somehow, they just aren't a Religion of Evil. They aren't taking over the world because their religion says that taking over the world just isn't the right thing to do. Nor are they overtly evil; oh sure, they perform acts of unthinkable depravity in the name of their God, but they aren’t just doing it For the Evulz... they actually have a well-thought out and defensible reason for doing what they do.

Sometimes, in fact, morality plays absolutely no role at all in their ideology. The followers of the religion don't claim to have transcended the silly dichotomy between good and evil, nor do they think of themselves as impartial mediators between warring factions. Rather, the concepts of good and evil just don’t occur to them. If you asked them what they think of the whole good/evil thing, they'd look at you incredulously, as if you just asked them where their religion stands on the issue of albino octopuses named Jerry.

You could probably cite Culture Clash and write this entire religion off as primitive and uncivilized, leaving them to their own devices, if they weren't in the habit of committing unforgivable atrocities in order to fulfill their ends.

The xenophobic form of this religion tends to have a full system of morality and justice for its own believers, who never think of extending the same courtesies to others. However, the religion may in fact lack any recognizable form of prejudice, in much the same way that humans rarely feel speciesist when swatting a fly.

Works very well when all the members of this religion were brought up in a mono-religious culture. If the god (or gods) of this religion actually exist, they may not actually endorse the behavior of their believers — though they may also be sufficiently alien as to be completely uninterested in morality (or at least morality as we know it). Tends to overlap with the "Aliens as Religious Fundamentalists" form of Scary Dogmatic Aliens — massive cultural dissonance is easy to explain away when it is the byproduct of bizarre alien psychology, and it reduces the danger of the heroes capturing and instantly converting one or more of the zealots by simply pointing out that they're hurting people.

If the long-term goals of the religion's dogma include freeing their God of Evil from his long imprisonment so that he may resume his reign of terror, then they're doing so not because they're deluded into believing that their god is made out of happiness and rainbows or because they plan to become his unholy rampaging army when he returns. Instead, they probably don't have any long-term plans once the magical shackles are broken. There may be a Roaring Rampage of Revenge, but it's the god's revenge, not the worshippers'.

If the believers of this religion honestly think they're doing the right thing, then you're probably looking at a religion of Knights Templar. If the religion intentionally "goes for the evil points," or if the religion's dogma has no purpose besides simply promoting evil, then you've found a Religion of Evil.

See also Moral Myopia and Blue and Orange Morality. Compare Religion of Evil and Path of Inspiration. Contrast Scam Religion, which is simply empty.

No real life examples, please; most examples would be rooted firmly in highly subjective opinion and only serve to fuel flame wars. The rest would be about Scientology.

Examples of Scary Amoral Religion include:

Comic Books

The Skrulls of Marvel Comics' Secret Invasion claim that they own the earth because their religion says they do.

Fan Works

In the classic Star Trek / Babylon 5 crossover story, A Thin Veneer, the Ashen are an offshoot of the Minbari who literally worship the Vorlons as Gods. Their religion tells them that they are the most superior beings in the Galaxy because of this, and that they cannot be defeated thusly. They hold onto this view even as the Federation constantly curb stomps them.

Film

The atomic-bomb worshipping mutants from Battle for the Planet of the Apes.

Literature

The Star Wars Expanded Universe has the Yuuzhan Vong, who are in the market for a new galaxy and have just found this very nice one in which most of the inhabitants happen to depend on one of the central heresies of the Yuuzhan Vong religion—the use of non-organic technology. (Not to mention that they all have quite the wrong understanding of pain- pain is sacred and to be cherished, not avoided!) The solution? Mass xenocide. So it goes.
The various cults from the Cthulhu Mythos tend to fit this rather well. They're not usually evil per se, just like their god aren't actually evil (exept for Nyarlathotep, and even he's more of a dick than truly evil). According to one cultist being interrogated in Call of Cthulhu, the cultists wish for the Old Ones to return so that they can make mankind like them, unbound by law or morality, and free to dance, laugh and kill as they see fit.
Thulsa Doom's Serpent Cult from Robert E. Howard's Kull stories (as well as some adaptations of Conan, such as the movie which was originally to be about Kull anyway).
In Alan Dean Foster's The Damned Trilogy, "The Purpose" is a religion promoted by the bad guys in which all sentient life in the Galaxy comes together in cooperation by abandoning freedom and free will. And the purpose of this cooperation? To force those species who don't necessarily want to be a part of the Purpose to join up or die.
The Howlers from Animorphs may count. Their "god" really is evil, but a theme of the novels is that no sentient species can be Exclusively Evil, forcing him to resort to this. Essentially, the Howlers are able to slaughter every other race in the galaxy without mercy because they have the minds of children and no idea other species have any sentience of their own.

Live-Action TV

In the Doctor Who episodes "Bad Wolf" and "Parting of the Ways", the Daleks seem to be worshipping the idea of their own perfection. The fact that the Daleks have a concept of blasphemy absolutely horrifies the Doctor.
The Goa'uld and their followers in Stargate SG-1 fit this trope pretty well but the Ori fit it even better, all the way down to disputes over the meaning of symbolic passages in the very King James-sounding Book of Origin. The Goa'uld aren't so much dogmatic as create dogma around themselves to control their underlings. The Ori, on the other hand...
In Star Trek: Deep Space Nine, the Jem'Hadar worship the Founders of the Dominion as gods, and see the was on the Alpha Quadrant as a holy crusade. The Founders are said to have an innate need for order and conformity, and the avowed mission of their crusade is to bring this order to the untidy quadrant-next-door.
In Babylon 5, the Minbari war against humanity was seen as religious crusade to avenge their "holy leader" after his death in a botched First Contact encounter.
- On a lesser scale, an alien couple murdered their child after he underwent surgery, because their faith declared that it made him "empty".
The Soldiers of the One in Caprica are a monotheistic cult in a polytheistic society that believes in absolute black and white morality, and some of their branches are perfectly willing to practice suicide bombings for their beliefs, while the others quietly approve of their actions. It also seems that the Cylons inherited some of their ideology and dogma, and used it to justify the attempted destruction of the human race in Battlestar Galactica.

Tabletop Games

In Warhammer 40,000, the Church of the God-Emperor is the main inspiration of its many followers to go to war, and a secondary inspiration for many other factions. The Church is xenocidal and imperialist, and as happy to wipe out a wayward billion of its own people as it is to exterminate entire alien races, sometimes even for a perceived slight.
- Eldar also have their own Eldar-centric religion. Eldar religion (or the surviving bits of it) has essentially two parts: one requires Eldar to survive at all costs until their new god can emerge, namely costs callously paid in billions of lives of other species, and the other part consists almost exclusively of war and murder.
- The Tau are arguably a subversion, being a race of Flat Earth Atheists in a setting where literal daemons are an active force. They are regarded by the Imperium as being completely heathen, believing in no supernatural forces whatsoever. However, they are also philosophists, following strongly to a collectivist creed of striving for the Greater Good, beliving that they should share this philosophy with every other sentient in the galaxy and that Utopia Justifies the Means in doing so. This tends to put them squarely into Scary Dogmatic Aliens trope, but with the twist that their dogma is secular in a setting where supernatural forces are real.

Video Games

The Zerg from StarCraft exist for no other reason than to assimilate any species that improves their genetic stock that they encounter on their interplanetary crusade. Every sentient Zerg on the upper levels of the Hive Mind exists to participate in a religion centered around their overarching consciousness, the Overmind. The first partially free-willed consciousness that enters the Zerg Hive Mind apart from the Overmind itself (Kerrigan) eventually breaks away from the Overmind and becomes wholly and unapologetically evil while constantly lampshading the fact.
The Eternal Doctrine and the Path of Now and Forever from Star Control, both of which treat Ur-Quan security as paramount. The Kzer-Za's Path of Now and Forever decrees that every species is a threat to the Ur-Quan (because it might someday become too powerful if left to its own devices) and therefore must be subjugated. The Kohr-Ah Eternal Doctrine is similar, except its answer to these threats is not subjugation, it's annihilation. It's all good, though — since they believe in reincarnation, species they "cleanse" will have a chance to be reborn as Ur-Quan eventually.
- Their respective philosophies are a direct result of their former slavery to the Dnyarri, who used genetic engineering to split one Ur-Quan species into two. The Kohr-Ah were soldiers, and their Eternal Doctrine reflects their simple worldview - eliminate any threat. The Kzer-Za were administrators and scientists and do not discount the benefit of having slave races and have a better understanding about controlling them. When the Kzer-Za armada surrounded the Syreen fleet (all that remained of their race) and received their surrender, they went out of their way to find them a suitable planet as the new Syreen homeworld. Also, instead of destroying all Syreen ships, they mothballed them, just in case.
The Children of Atom and the Apostles of the Holy Light from Fallout 3 are a sort of subversion: both have an unhealthy relationship with radiation, but they're a nice, good religion.
- Well, the Children of the Atom are pretty much harmless. The Apostle of the Holy Light, on the other hand, had taken to handing out water imbued with lethal levels of radiation to unsuspecting travelers without their knowledge, because they believed that irradiating their bodies would save their souls.
The Covenant are out to Kill All Humans because their religious leaders have declared humans to be an affront to their gods. It is revealed in Contact Harvest that humans were the chosen inheiretors of The Forerunners whom the Covenant base their faith upon, and that knowledge of this among the Covenant would have undermined the Covenant's leaders (the Prophets mostly )of their claim to power and the entire society would collapse.
The Order from the Silent Hill series either falls under this trope or under Religion of Evil. Sure, their leaders Dahlia Gillespie seems to want and Claudia Wolf definitely craves a paradise for all humanity, but members like Leonard Wolf take a far more militant and unforgiving stance while even Dahlia gets at least a little giddy at the thought of a violent apocalypse. Plus it doesn't help the argument that the Order is basically well-intentioned that in Silent Hill 4 it's revealed that the Order runs an Orphanage of Fear that makes the Oliver Twist orphanage look like the fireworks, candy, and puppy dog store.
Supreme Commander the Aeon Illuminate who follow a religion called The Way, their main goal is to spread the way to humanity, but are willing to cleanse all non-believers.