The world often notes that certain groups take God and Guns with equal fervor. The Church Militant takes this observation to the natural conclusion, a Catholic (or Catholic-like) superpower that is very heavily armed. This can be played in any number of ways- Light isn't always good, and even when it is, Good is not always nice, and even when it is, Good isn't soft.
Usually justified by the actual existence of witches, vampires or The Legions of Hell; nevertheless the Church Militant often struggles with going too far. Don't expect heavy consistency with real world religious teachings, writers will make it up as they go along (c.f. The Lowest Cosmic Denominator). Anime will just substitute in that Nuns Are Mikos.
The forces of a Church Militant vary widely depending on the nature of its foes and the type of world it exists in.
The most commonly associated troops for the Church Militant are its heavily armored, sword-slinging, holy-equipped special forces usually known as Paladins. Nuns with guns usually come halfway between this and Amazon Brigade. If there is a Fanatic branch of the Church Militant, expect the Knight Templar, but also expect their zealotry to be tempered by the church heirarchy- orders with divine authority behind them are hard to ignore, and there is usually a larger war to win.
In a modern industrialized setting most clergy will rely on Hand Cannons, but since many breeds of Undead and Eldritch Abomination are Immune to Bullets, expect at least a few priests and nuns of The Blessed Blade Sect to swing around a broadsword or two. Or three/six, which seems to be some kind of standard.
Oftentimes, they might instead favor the mace, hammer, or staff out of an alleged commitment to peace. This doctrine is espoused by the Order of the Blunt Instrument because theoretically bludgeoning weapons allow for "just" beating the hell out of an opponent, and they take a "strict" view of the commandments against "spilling blood" or "taking up the sword." Also blunt weapons are cheap, and there are vows of poverty to consider.
In fantasy settings they'll probably also have divine magic, most often White Magic, but when the Church militant is played as also being the Corrupt Church, Black Magic may be used alongside or even substituted. Even in settings featuring a purely good church militant, the light side's magical bag of tricks isn't limited to Healing Magic, stun spells, and summoning puppies and rainbows- concentrated blasts of goodness, cleansing light, and Bolts of Divine Retribution are standard issue for The Order of Smiting. In the more liberal chapters, such as the Brothers of the Clandestine Operations, one might even find instances of The Sacred Darkness being put to work on the side of the faithful.
In more critical scenarios involving The Legions of Hell running rampant and hordes of undead terrorizing the countryside, Holy Hand Grenades are mass produced, as are weapons Made of Good or Silver. In case of Witch incursions and Heresy, expect Flamethrowers and Flaming Swords. Lots and lots of flame-based weapons to purify the sinful. And you can be sure that there are at least a few Fantastic Nukes among the church's relics because there's only one way to be sure that nothing will ever use thatHell Gate again.
Individual members are usually Hunters or Warrior Monks and can also be referred to as "church militants" (where "militant" is the noun). Note that this trope really only applies to Western theist/deist religions, as Eastern religions (Buddhism, Shinto, Tao, etc.) are almost always depicted as kung-fu-slinging warrior monks (sometimes Christian/Pseudo-Christian monks can be kung-fu-slinging as well).
If a Church Militant exists as a State Secsubdivision of a larger, predominantly pacifist Church, expect it to be called "The Inquisition" regardless of the fact that Real Life inquisition was more like a detective and judicial branch of the Catholic Church (see also The Spanish Inquisition) than its military arm. See also Kung-Fu Jesus.
Not to be confused with Corrupt Church, where the religious folks are clearly the bad guys. Badass clergymen who are minorities amongst a meeker lot would be Badass Preachers instead. Also not to be confused with the actual Catholic concept of the Church Militant which comprises all believers still on Earth, as compared with the Church Triumphant, the believers in Heaven. Here, the "militant" refers not to actual violence but the spiritual combat that believers undergo to thwart the Devil and his temptations so as to become a member of the Church Triumphant.
The moral questions surrounding the idea of religious authorities advocating violence have been around since the beginning of monotheism. Polytheistic religions generally don't result in Moral Dissonance, instead delegating war behavior to deities who are specifically devoted to kicking ass. Monotheistic religions, on the other hand, have always had the problem of reconciling a loving God (assuming He is loving to begin with) with the specifically unloving human behavior that is intrinsic to warfare. Sometimes it is based on the idea that wrongdoers and criminals, domestic or cosmic, lose variably some or all of the protection of God and society because of their bad actions and therefore should come quietly or be defeated. There is the philosophy that self defense and the defense of others from bad guys - out of love for others - is acceptable and just in God's sight. It must also be understood that soldiers face death every day, and naturally have a vested interest in spiritual pursuits. Also, in general, non-Christian religions portrayed as Church Militants are usually frowned upon.
Church Militants often make use of Smite Evil. The smitees may not appreciate this, and may strike back, e.g. through Religion Rant Songs or other means.
Has some overlap with Naughty Nuns, often in the form of 'Nunsploitation' films. One of the groups you may ask Who You Gonna Call? when the Forces of Darkness strike.
For whatever it's worth, "Church Militant" is a Catholic term for the community of Christians – usually meaning Catholics specifically – currently engaged in spiritual "warfare" (in Latin, militant literally means "serving as a soldier") against sin and temptation on Earth – i.e, living Christians – as opposed to the Church Triumphant, who are enjoying their eternal reward in Heaven, and the Church Expectant or Penitent, who are undergoing temporary purification in Purgatory before upgrading their accommodations.
Sakura Wars: A variation; Erica Fontaine is both a nun and a member of the Paris Assault Force; the convent she belongs to is not a military organization in itself.
Hellsing has both the Anglican Church and Catholics forming their own Churches Militant. Accusations of heresy and territorial claims mean their militants often clash if they meet, but they will sometimes delay fighting each other to fight vampires. Sometimes. Doesn't help that their trump cards display a Blood Knight mentality and will fight at the drop of a hat. The series eventually climaxes with the Vatican's 9th Crusade against the Nazis and, eventually, all of Protestant England. Maxwell even takes advantage of London's vulnerability to slaughter Protestant civilians, all in the name of God and the Catholic Church. Thankfully, Father Anderson does not agree with that last option.
Blue Exorcist have the True Cross Order, a Badass Army of Exorcists from multiple religions confronting demons and such.
Chrono Crusade features a religious order whose role is to serve as the Church Militant. As one might expect, the main character is a member of said order. The Order tolerate Rosette's Deal with the Devil on the grounds that 1) he's a sweetheart, okay? 2) the girl has a mission and she can't get out of it now, anyway, and 3) look, demon kill demon, we happy, okay? Until Remington is forced to stage Chrono's death in the manga. Her immediate superiors don't object, but the higher-ups have gotten twitchy. Good times had by all as the good Father more or less pounds Chrono in the head with the situation after cool hints don't work.
In Trinity Blood, the Vatican is one of the two major world military powers, the other being the vampire-led Empire. The latter, being based in Byzantium, bears a certain resemblance to the home base of the post-schism Eastern Orthodox church.
Nicholas D. Wolfwood, and specifically the Eye of Michael group from Trigun. The latter are plant worshippers, which explains why they're willing to work for Knives. The representatives we see don't appear to worship anything except Gorn and More Dakka. And posibly For Science! in the case of Original Chapel. Makes you kind of relieved that Wolfwood is so laid-back about his faith.
Tsukihime and Fate/stay night, which take place in the sameworldmultiverse, have a secret church organization that hunts down heretics, which includes undead and rogue sorcerers. An example is Ciel. The Vatican consider it borderline heretical, due to its activities.
The nuns on the Mahora campus of Mahou Sensei Negima! are all trained battlemages who make up school security in addition to more traditional duties.
Altena's faction of les Soldats in Noir aka "The Nuns With Guns".
The Ishvalans in Fullmetal Alchemist have warrior-priests, followers of Ishvala who are also martial arts experts. It was stated that during the Ishval rebellion an unarmed Ishvalan warrior-priest could take down 10 fully armed Amestrian soldiers. Scar was a particularly strong one.
The original Moetan book's entry for the word "priest" recalls this trope: "The priest has a cross-shaped bazooka." Given its penchant for references, this is almost certainly an allusion to Wolfwood.
Mozgus in Berserk fulfills this trope together with his followers. They take great pleasure in killing and torturing "heretics" at will. There's also the Holy Iron Chain Knights, a church-serving order of warriors who are mostly ornamental but nonetheless quite capable of kicking ass.
Black Lagoon has the "Church of Violence''. While it's unclear whether its members are actually religious or are just using the Church as a front for weapons smuggling, it still doesn't stop its members from toting a ridiculously massive arsenal of weapons such as M60 machine guns and a gold plated Desert Eagle (wielded by a 70 something nun with one hand).
Subverted in JoJo's Bizarre Adventure. While Enrico Pucci is an evil fighter priest, it is not out of fanaticism. In fact, he is a heretic who worships an evil vampire and abuses his status as a priest.
Church Militant still holds. As his twin brother Weather Report (yes, that's his name) said, Enrico Pucci is not aware that he is evil. Which makes him creepier because he believes he's doing all these beating up prisoners, pitting them against each other, siccing a gang on Weather Report to prevent his incestuous relationship with their little sister (both Weather and his sister were unaware of this incest), collecting Dio's sons, trying to revive the world without the Joestars... for the good of mankind.
Justin Law from Soul Eater is the Deathscythe in charge of Europe, dresses as a priest and is a very devout follower of the shinigami, who has been shown to be considered a living deity in the Soul Eater universe.
Recent events reveal that Justin has apparently turned his allegiance to the other side. Oh, and his new boss has kidnapped the Jesus of his religion.
To Aru Majutsu no Index. Necessarius and most of the Church Organizations in Necessarius are a group of battle-priest/mages that protects England and the Puritan Church from any magical and scientific threat by using the one thing they tried to destroy in the past: Magic. They're also responsible for the compilation of Index-Librorium-Prohibitrum in Index's mind. There are three notorious Churches:
The Anglican Church, with Necessarius.
The Roman Catholic Church, with Agnese Forces and God's Right Seat.
Subverted in Simoun, where the church itself doesn't like that the military is forcing them to use their priestesses as killers, even if their prayers happen to be the most effective weapon Simulacrum has.
Subverted with Mobile Suit Gundam Wing's Duo Maxwell; though he wears a priest's collar and kicks a lot of ass, he doesn't actually make any kind of big deal about religion. In his backstory he was an orphan raised in a church, but one day tells the priest he doesn't believe in God but he does believe in the God of Death because "I've never seen a miracle, but I've seen lots of dead people!" (The good-natured priest admits that he can't fault the boy's logic.)
Somewhat ironic considering Duo later grows up and becomes a legitimate priest himself.
Warrior Nun Areala by Ben Dunn, an animesque comic focusing on a Catholic order of monster hunters. Before anime/manga (like Chrono Crusade) or western comics, this series was the first to focus on such a topic.
William Stryker◊, an infamous X-Men villain, is a Christian fundamentalist televangelist who saw himself on a mission from God to eradicate the mutant race. During the "Second Coming" storyline, Stryker was shown to have a literal army of members from his "Church of Humanity", who used high-tech lasers and "weaponised rituals" against the mutants. The version in X-Men 2: X-Men United discarded this aspect, making him just a plain old militant.
In one storyline, Nightcmrawler takes steps to become a priest.spoiler: - click to reveal It turns out he's been mentally controlled into thinking he's becoming a priest by an extremely militant vaguely Catholic organization that plans to make him pope, and then use some sort of explosive-laced communion wafer that disintegrates people. This will then be the sign that the rapture has come and Nightcrawler's image inducer will be short-circuited, revealing his demonic appearance and leading everyone to believe the anti-Christ has taken over the church. Catholics don't actually believe in the Rapture, but still... anyway, it features a very militant church attempting to effectively take over the world.
Magdalena (originally from The Darkness), somewhat similarly, is a name passed on from generation to generation of nuns in a certain order that claims to have begun with Mary Magdalene herself.
The Badger had a recurring character named "Sister Twister", a reformed Nazi transexual nun.
There's also a Sister Twister who was in the latest incarnation of the Suicide Squad. A woman with distorted features and the power to painfully contort other peoples' bodies, she found God and became a nun. However, her supervillain sadism is still not fully dulled; when asked if the old axiom of "it's better to give than to receive" also applies to pain, she responds that while she hadn't thought of it that way she's very interested in applying it.
Canon Fodder takes place in a future where the church and police forces have been consolidated into one, and follows a single very devout, not entirely sane priest as he attempts to destroy evil wherever he finds it.
The Ghost Rider comics give us the Deacon, a monster of a man who is so devout in his belief that he is saving sinners the Penance Stare has no effect on him. He eventually fights a nun-turned ally of Ghost Rider, with the Pre Ass Kicking One Liner of "Very well, woman. Let us pray."
The Confessor and the Crossbreed from Astro City. The Crossbreed in particular come off as a bunch of annoying fanatics. Initially.
Father Zee in Ex Machina. During a riot, someone yells out "RAISE HELL". Father Zee sucker punches him right in the face and says "If you say so". He frequently spars with Mayor Mitchell Hundred.
Savage Skies has the Cult Solar as one of the primary antagonists. Interestingly, the majority of the cult is not comprised of soldiers, it's just that Dawn Lightwing happens to be considered a demon and the ponies on top are willing to utilize lethal force.
The Boondock Saints are a variant of this trope. They don't fight the legions of hell (or at least not in any demonic implication), but they do themselves state religion as their reasoning (the 'inspirational' speech from the priest at the beginning) and go so far as to say their family prayer over their victims. It's also strongly implied they that they believe they are administering God's justice to evildoers.
The Grammaton Clerics of Equilibrium use the trappings of this trope, although they serve a secular state.
Something of an example occurs in two of the Trinity Spaghetti Western films.
In the first movie, Trinity and his brother Bambino (both are criminals themselves) assist some Amish settlers in fighting off Mexican marauders who take advantage of their vow of peace. By the end of the movie, Bambino and Trinity have taught the religious people how to defend themselves. The movie ends with the Amish people making a stand for themselves and defeating the Mexicans.
In the second movie, Trinity and Bambino wind up in a monastery where several criminals are hiding and pretending to be monks. When Bambino asks the true monks to raise their hands, everyone raises their hands. Trinity responds by saying, "Every monk who is a monk, hit a monk that ain't a monk."
The organization Van Helsing works for, comprised of the Vatican and representatives of other religions from around the world: one of their blacksmiths was noted saying "what in the name of Allah"
To be fair "Allah" is the Arabic word for "God", with no specific ties to any particular religion.
Priest has this in spades. The titular "Priests" are a team of specialised, superhuman Vampire Hunters who are so aligned with combat that they have trouble fitting in when they are not needed.
Stranger in a Strange Land features "Fosterism", a parody of American tele-evangelism on one level but very much Church Militant in a political sense
The two Endymion books by Dan Simmons feature a rabid Vatican that exploits the resurrecting power of alien cruciforms to grant believers immortality. The Pope heads an aggressive crusade against "heretics" with interstellar warships, manned by Swiss Guard special forces.
In Bernard Cornwell's Saxon Stories, there is a certain Father Pyrlig, who relies on people assuming fat men can't fight. Usually by the time they realise that they can, they're dead. There is also a One-Scene Wonder Abbot, an ex soldier who the main character notices is carry a BFA (Like BFS but with an axe), a heavily used one with notches. When the narrator enquires after it, he is cheerfully told, "It is sent many a pagan to Hell, Lord." Since the Abbot has a large scar on his face, you believe it.
The Faith Militant, or Swords and Stars, in A Song of Ice and Fire consists of two armed orders: the Warrior's Sons and the Poor Fellows. The former is made up of knights and nobles, while the latter's members are commoners. Both of these orders were banned for over two hundred years, but Cersei Lannister resurrects them as part of a political bargain with the Faith. The carnage of the ongoing wars creates a major revival in religious fervor, causing both orders to swell in rank and rapidly become uncontrollable. By the end of A Feast for Crows, the results of an implosion of machinations include Cersei being arrested by the Faith.
David Eddings's Elenium uses this heavily, with most of the major characters being either members of or otherwise involved with the Church Knights. The four Orders of the Church Knights are an organization of elite trained mage-warriors who were created to defend 'the West' from the sorcerers, demon-summoners and necromancers of the Evil Empire and its Cthulhu-esque god. The irony...they get their divine/magic powers from a different god than the one they supposedly worship; they don't worry about it. Amusingly, a proposed experiment with drawing upon the power of their own God (who is, after all, one of the most powerful and most distant deities) is quite strongly rejected by the party's clergyman.
Eddings plays this on both sides of the coin, really, as the Belgariad/Mallorean's Torak had the Grolim priesthood, and all of Cyrgon's priests in the Elenium/Tamuli were warriors as well. Even the evil god Azash tried this as well, as a counter to the Church Knights, but neither Azash nor his high priest Otha could really comprehend the realities of it; the former was too elemental-minded and the latter was... well, to put it bluntly, too stupid.
The Elenium actually has several examples. The Church Knights are the most visible within the narrative, technically cloistered orders who are also exceptionally skilled fighters but there are also two other groups. The first and most numerous are the Church Soldiers, lay members who serve as guards for assorted Church leaders and properties, many of whom are little better than mercenaries in the employ of corrupt Church officials. The last is a small group dedicated to protecting and guarding the local pope analogue and have a much better reputation in terms of personal integrity.
Brothers Benedict and Tobias of Revelations hail from such a group, which amazingly avoids being a gathering of Well Intentioned Extremists, though more because all the "heroes" of Revelations do nasty things from time to time than from their own moderation.
Both played straight and subverted in The Dresden Files with the three Knights of the Cross aka Knights of the Sword. Michael, the most prominently featured Knight, is a devout Catholic who fights demons, fallen angels, ghosts, vampires, dragons and evil sorcerers with a divinely powered sword and improbable luck courtesy of divine intervention. However, the other two Knights are a) a self-proclaimed agnostic who fights evil purely for the sake of serving the common good, and b) a Japanese man who was only baptized by accident (but tries to be a good Christian anyway now that he is one). Averting the usual Knight Templar tendencies of Church Militants, all these Knights are practically Messianic Archetypes and try to save even the most twisted and corrupted of humans even if it means risking their lives for it. In fact, it's in the job description.
In short story "Warrior" we meet Father Douglas - U.S. Army chaplain, parish priest in Guatemala, Indonesia and Rwanda, sniper for the rangers, trained in demolitions, knowledgeable in magic. He's so ruthless that his handlers in the Ordo Malleus stop supporting him.
The Omnian theocracy in the Discworld novel Small Gods - combines the military-imperial aggression of medieval Islam with the paranoid doctrinal intolerance of medieval Catholicism. After the events of the book the religion mellows out somewhat, but is no less aggressively evangelical, so now Omnians travel door-to-door to distribute religious pamphlets and talk to people about Om. Most of their neighbors view this with equal dread, and end up hiding behind furniture when they see Omnian priests headed their way.
This even extends to naming their children things like "Visit-The-Infidel-With-Explanatory-Pamphlets and "Smite-The-Unbeliever-With-Cunning-Arguments".
Mike Carey's Felix Castor novels has the Anathemata Curialis, a militant and officially excommunicated group fighting the return of the undead, partly by using the undead themselves, or any other means available.
The Children of the Light/Whitecloaks in The Wheel of Time, a militant religious organization resembling the Knights Templar and Crusaders and mainly dedicated to calling people Darkfriends and executing them for looking at them funny, besides calling all the magic users (Aes Sedai) witches and assassinating or outright killing them whenever possible. Despite every other country but Amador (their base) hating their guts, they are for some reason given free passage into any country as long as they are only in small numbers (however they break this rule constantly), and don't cause any trouble (again, they break this rule constantly). It is mentioned that 50% of the common people supposedly like them, which may be the reason rulers tolerate them, but Jordan never bothered to show any common people doing anything but cowering in fear when they come by, so...
At one point Thom Merrilin's reaction to a statement by Elayne suggests that the Lord Captain Commander of the Whitecloaks, then Pedron Niall, was close to or more powerful than the Queen of Andor, one of the more powerful of the nations, as there are apparently Whitecloaks in and from every land. The 'from' bit is as close as indicating they have large scale support as exists one supposes.
The Little Sisters of the Immaculate Chainsaw in Simon R. Green's Nightside books.
Also the SAS (Salvation Army Sisterhood). Hard-core nuns of military persuasion, that have been banned and condemned by every branch of Christian Church (though, they still hire SAS when all else has failed). SAS burns down satanist churches, perform exorcisms on politicians and they once skinned and ate a werewolf. Save them all and let God sort them out, so to speak.
Turpin, Archbishop of Rheims, and Don Jerome, bishop of Valencia after its conquest, serve as examples of this in the tales about Roland and El Cid, respectively. Both apparently used swords, at least in the stories.
The Twisted Cross in the Wingman series by Mack Maloney features friars in the South American jungles who defend their mission from regular raids from bandits and Neo-Nazi invaders. A group of them, including their leaders, later join the protagonist on his journey to stop the Nazis from finding hidden Incan gold to fund their war effort and plant nuclear mines in the Panama Canal to keep control of it.
Cestus Dei, by John Maddox Roberts, set in a far future when a heavily reformed Catholic Church is a major spacefaring military power.
The short story "The Way of Cross and Dragon" by George R. R. Martin. The protagonist is a Catholic Inquisitor traveling among (mostly) human colony-worlds to put down heresy.
Gordon Dickson's Dorsai series has the Friendlies, on the planets Harmony and Association, exemplify this trope. The planets constantly have wars between the various sects. Oh, the Friendlies are also hired out as Cannon FodderMercs, their only major export.
David Weber uses this trope a lot in his various stories.
In his novel Crusade in the Starfire series, an alien race believes that Earth is their heaven and that humans have poisoned it so they go out to take care of things.
In his Safehold series the main villains are the corrupt heads of the Church of God Awaiting, who have deified the very person to have orbitally bombarded the planet and sent them back into medievalism centuries earlier.
Specifically the Temple Guard which forms the backbone of their forces as well as providing the role of the military equivalent for the lands directly administered by the Church.
Yet another example in The War Gods Tomanak, the local war god's has the most notable on in his Order, but other deities are mentioned to have their own, smaller fighting forces, such as the Axes of Isvaria to name but one.
In John Barnes's Sin of Origin the Christian Commonwealth has a renewed Knights Templar as its military wing. They're actually the good guys, more or less.
The Fraternity of the Stone (from the book of that title by David Morrell), a secret society dating back to the Crusades created in response to the Assassins. In modern times they serve as an intelligence (including assassination) arm of the church.
The Derethi from Elantris are a deeply hierarchical and militant religion, with their priesthood resembling a military as much as a clergy. Derethi high priest Hrathen is perhaps the single most dangerous combatant of any of the main characters save one, and don't even start on the DakhorMonks...
Lois McMaster Bujold's Chalion series features two groups of church militants. In the polytheistic Quintarian religion, men who pledge their oaths to The Son of Autumn are the Army, while those who join the order of The Daughter of Spring maintain order within the country's borders.
A character in Tamora Pierce's Provost's Dog series mentions "warrior [women] with sickles" from a temple who punish violations of the "Goddess's Law concerning women." Given that said priestesses are mentioned in reference to a man notorious for roving hands, it's not hard to imagine the gist of the Law. The Goddess' temple warriors are mentioned in other Tortall books, too.
In JH Brennan's Barmy Jeffers books, there is a literal Church Militant. Motto: "Bless 'em! Bash 'em! Hack 'em! Slash 'em!"
It's worth noting that because the Barmy Jeffers series was a conscious spoof of various tropes associated with Tabletop Roleplaying (and especially Dungeons & Dragons) this was a deliberate reference to D&D-style "Cleric" characters.
Seret knights in The Riyria Revelations are the Nyphron Church's (and eventually, New Empire's) enforcers-cum-inquisition, beholden only to the Patriarch and Sentinels.
Special Circumstances: While the members of the titular organization do "kick ass for the Lord" (or whatever deity[ies] they may worship), it's not done specifically in service to their religion.
The Church of Lumin in Stories Of Nypre may not seem militant at first. Then you realize the priestesses who run the place also serve as commanders of Lumin's army and are quite quick to dispatch them in an attempt to control magic in the world.
The demonic narrator of The Screwtape Letters describes the church as seen from the spiritual dimension (where things that seem mundane to humans, such as a simple prayer, take on very real and tangible consequences) this way:
“…the Church as we see her, spread out through all time and space and rooted in eternity, terrible as an army with banners…"
The Minbari Religious Caste in Babylon 5. They hold off the shadows practically on their own. While the warrior-caste stays home.
One episode of Supernatural featured the Covenant Lutheran Militia who patrolled with a fire-truck filled with holy water.
The Doctor Who episode "The Time of Angels": "Father Octavian, Sir. Bishop, 2nd class. Twenty clerics at my command. The troops are already in the Drop Ship and landing shortly." According to the Doctor, "It's the 51st Century. The Church has moved on."
The year afterwards, we got a villainous example in "A Good Man Goes To War". The rank-and-file soldiers mostly seem like ordinary people (there's even a married gay couple), but the Headless Monks are — well, the name kind of sums it up. Oddly, they seem to be made up of different denominations — the married couple are Anglican, but their colonel refers to a "Papal Mainframe". (Granted, the same colonel mentions the Queen and its three thousand years in the future so it's not too unreasonable to suppose that the Catholic and Anglican churches have merged, along with the Army by then.)
The army in A Good Man Goes To War is explicitly a task force made out of a levy of allied political entities with the specific aim of taking down The Doctor. The "Gamma Girl" is from a world that is mentioned as being "Heaven Neutral" making her presence odd, since they apparently aren't involved in this conflict. This could mean that most soldiers at this time in history are "clerics", or, possibly, that the conflict with the Doctor is a holy war that all the denominations have agreed upon.
"The Time of the Doctor" featured the Papal Mainframe (first mentioned in "A Good Man Goes to War"; Colonel Manton's edict to lower the Headless Monks' hoods came "by the divine grant of the Papal Mainframe herself" and revealed that it is actually a massive space church built into a starship, and that it is commanded by an old friend of the Doctor's named Tasha Lem. The church functioned as an "intergalactic UN", and strove to maintain peace and security. Although at first benevolent (like the clerics seen in Series 5), they and the Doctor became entangled in a predicament which prompted Tasha to issue an "unscheduled faith change," dedicating the church to the purpose of keeping the Doctor from speaking his name on Trenzalore to release the Time Lords (which would incite another Time War), and declaring that only the Doctor's silence would fall on Trenzalore. It was also revealed that the memory-proof Silents that appeared in Series 6 are the church's genetically-engineered "confessional priests," and that the iteration of the church that was seen in "A Good Man Goes to War" was a Renegade Splinter Faction led by Madame Kovarian that resorted to extremism in order to maintain the Doctor's silence, by traveling back along his timeline and attempting to kill him before prematurely (via blowing up his TARDIS in Series 5 and training River to assassinate him in Series 6) so that he could never go to Trenzalore in the first place (although, in reality, they just ended up creating the very situation that they were trying to prevent).
In BattleTech, Clan Cloud Cobra are known for as "the clergy of the Clans". Being founded by a Chaplain, the Cloud Cobras all follow a ecumenical religious movement called "The Way', although they have subdivisions based on Christianity, Judaism, Islam, and other faiths.
Comstar and its offshoot, the Word of Blake, who elevated the preservation of knowledge to a religion — then started nuking people. Comstar's own army, hilariously enough, were composed of people that were Mechwarriors first and lacked the fanaticism found in other Comstar branches, as well as seeing machines less as objects of reverence and more as tools they're quite fond of. When the zealots broke off and formed the Word, the Com Guards had the smallest losses of personnel.
Of smaller scope is the Brotherhood of Randis, a small and exclusive order of philosophical and devout Christians. Originally little more than a mercenary unit with high ideals and really bad management, since the 3050s they've become known throughout the Periphery for performing works of charity, setting up missions and schools, and dispensing brutal asskickings to pirates.
The Imperium is one massive Church Militant— the government wear habits (and brandish laser-pistols), while the police force is more concerned with heresy than crime. Ordinary Imperial planets hold colossal celebrations of the Emperor on innumerable Saints days (while brandishing yet more laser pistols). They also have a permanent Inquisition which acts as State Sec, armies of power-armored, gun- and flamethrower-wielding nuns, and a tremendous amounts of religious iconography and fanaticism that characterize the "normal" soldiers. This is probably a good thing, given that if you believe in false gods, the false gods can not only manifest in reality, but tear you a new bunghole in the process.
Sisters of Battle fit this trope moreso than any other Imperial faction, as their faith manifests as an in-game mechanic, as well as fighting with a Living Saint, the corpse of a martyr apparently ressurected through sheer force of will (or faith).
The Frateris Militia deserve a mention— badly equipped zealots raised at short notice by the Ecclesiarchy (Imperial Church, actually not much different from the Medieval Catholic Church 'IN SPACE!')
Chess— at least the standard version — gives us the Bishop. The French, however, call this piece the Fool instead, while the Russians call it the elephant, and the Germans call it the runner.
The cleric class in virtually all incarnations and permutations of Dungeons & Dragons. It seems that no matter what deity you serve, basic training in this class inevitably also covers melee combat with such weapons as your faith permits while wearing heavy armor. (Reinforced in the third and fourth editions of the game with additional combat powers, including ones specifically boosting the cleric's own butt-kicking prowess.)
There is also an NPC Adept class, which represents something closer to your average non-combatant cleric. It's just that your average PC is most definitely not a non-combatant.
And the Cloistered Cleric variant, who gets marginally more weapons and armor training than the average wizard.
From the Greyhawk campaign setting: Heironeous, whose clerics are soldiers, making them a literal Church Militant, Saint Cuthbert, whose followers can be ... enthusiastic at times about evangelizing, and who opposed evil with a passion, and Pholtus, whose inquisitions you probably don't expect, particularly from a non-evil church.
And the Paladin class, which is far more combat-capable than the Cleric class, and have the signature attack of Smite Evil(And its partner, Detect Evil), but are much more limited in spell range and have a much less powerful Turn Undead.
And, as of 4th edition, the Avenger class, who are clerics mixed with rogues to become assassins of God.
All clerics in the Eberron setting are holy knights, most ordinary priests are just adepts or experts. The Church of the Silver Flame are particularly well known for their zealotry.
Hunter: The Vigil has three of these: the Malleus Maleficarum, a secret arm of the Vatican dedicated to hunting down monsters (and usually of the "suffer not a witch to live" ethos); the Long Night, a loose group of pre-millennialist fundamentalists devoted to "redeeming" monsters; and the Knights of St. George, an Anglican group that focuses mainly on demons and sorcerers.
Also in the Old World of Darkness there's the Society of Leopold, your basic secret Catholic monster hunters.
And in the New World of Darkness, there's the Fire-Touched from Werewolf: The Forsaken, who act like this. One of the Pure Tribes that rejects service to Luna in favor of fighting the Forsaken, they see their undertaking as a holy cause and their tribal totem as a near-divine prophet. They're about equally happy to convert or kill their foes.
The Sisters of Mercy from the Feng Shui supplement Glimpse of the Abyss are a convent of Nuns With Guns based in the Netherworld who hunt down and kill those whom their Mother Superior deems to be deserving of the respite of death from the suffering the Sisters believe life to be. Those whose names end up on the Rolls of Mercy and are targeted for "deliverance" often aren't so keen on dying.
The Talislanta RPG allows players to become (among other things) any one of several types of intolerant cleric. Although few have any spellcasting abilities, these classes are interesting in that they are the only characters that come with the "torture" skill.
The parody RPG Macho Women With Guns has only three character classes: Bimbos, Succubi, and Combat Nuns. I'm sorry, "Sisters of Our Lady of Harley Davidson". Needless to say, that game is made of raw Awesome.
The Iron Kingdoms setting has a whole nation of these, called the Protectorate of Menoth.
Infinity gives this in spades. Most factions have either a Buddhist Catholic, Christian, or Islamic militant sect.
The Cyber Europe expansion to Iron Crown's Cyber Space RPG introduces some hotshot special forces of the Vatican, such as the Apostolic Carabiniers SWAT unit and a Mission-Impossible-ish intelligence service, managed by Jesuits. These organizations are consistently portrayed as (reasonably) Good Guys, which is surprising since the authors are all Swedes.
Additionally, the Cathars of the Church of Avacyn on Innistrad, bynecessity. In fact, the angels in Innistrad are also divided into several groups, and one of them, the Goldnight, is a Church Militant group.
Within The Dark Eye, there are numerous churches that fit this trope. The church of Rondra(goddess of honorable battle), the church of her son Kor(god of war, bloodshed and mercanaries) are at the forefront, but most churches have an order or two, that is more militant than the rest of the church.
Marie D'Artois in Anno1404 is very enthusiastic about leading the armies of the crusade, and she's damn good at it. This somewhat ironically makes her somewhat easier to manipulate, as she will do almost anything if adequately convinced it is what God wishes her to do: including destroy the homes of innocent people she's been lead to think are heathens.
Games of the Castlevania series set closer to the modern day depict "The Church" this way. Said church is rather open-minded, having "Church Witches" in high ranking positions. Not surprising; Dracula tended to kill off anyone the Belmonts weren't protecting, and they were fond of white-magic users, especially the Belnades clan. It's been retconned that Sypha Belnades worked for the Church and was on a mission for them when Castlevania III: Dracula's Curse took place.
The Belmonts themselves are descended from Leon Belmont, a Crusades veteran.
The Protoss High Templars from StarCraft qualify for this trope, since they're highly trained priests capable of summoning deadly thunderstorms out of thin air.
The Protoss army. Their footsoldiers are called zealots. As in religious fanatics.
The Ethos organization from Xenogears bears certain resemblances to Catholicism, and seems to have at least their fair share of firearms.
Bloodline Champions has the Guardian and Inhibitor bloodlines, which both are this in job description.
The Lord's Believers in Sid Meier’s Alpha Centauri are a faction of technophobic Church Militants. Their combat bonuses (from fanaticism!) keep them militarily competitive and, incidentally, make them scary fuckers if they manage to steal your weapons research. Which they will, because the same fanaticism makes them awesome spies (can't brainwash 'em, can't break 'em, and more than happy to die in the line of duty!). Or they just get Transcendence before anyone else and instantly win.
Also the Cult of Planet, who worship the planetary hive mind, and whose goal is to return Planet to its natural state...by any means necessary.
Likewise, in Sid Meier's Civilization IV, certain AI personalities (Isabella of Spain, for example) are religious zealots.
In Daggerfall, there were knightly orders associated with eight of the Nine Divines (Talos being a god hadn't been introduced to the series yet), which the player had the option to join on locating their chapter houses.
The Ordinators from Morrowind are a corps of elite guards/soldiers in service of the Tribunal Temple. The Temple also has the Buoyant Armigers, who are the private soldiers/agents of the "most stable" man-god of the Tribunal (Vivec, the two-tonal hermaphrodite poet god). There's also the High Ordinators, who are under the rule of the least stable one (Almalexia, the gold-skinned, red-headed ax-crazy warrior goddess). Then there are the Elites of those, known as the Hands of Almalexia: Six warriors with equipment enchanted by the goddess herself. All of them are said to be the most powerful warriors in Tamriel.
Also from Morrowind are the Imperial Cult "Shrine Sergeants," volunteers who take on some of the Cult's more action-oriented missions such as tracking down thieves who steal from the Cult or putting spirits responsible for hauntings to rest.
Oblivion had Weynon Priory, home to a few ex-Blades who manage to arm and defend themselves with claymores when attacked by the Mythic Dawn. One of the monks explains further that the Order of Talos and the Blades (the emperor's personal network of spies and bodyguards) are two arms of the same organization, and many members of one wind up in the other at some point.
In Sengoku Basara (Devil Kings to the western gamers) one of the characters is a missionary named Xavi (Q-Ball in Devil Kings), a Love Freak who dual-wields handcannons based on the foreign missionaries of Japan and whose goal seems to be the conversion of all of Japan (or whatever indeterminate country Devil Kings is supposedly in).
He doesn't appear in Sengoku Basara 3, but his influence remains in the form of Sorin Otomo, a powerful regional lord and one of Xavi's most faithful disciples.
The Apostles in Dreamfall: The Longest Journey serve as elite enforcers of the theocratic Azadi Empire. According to one of them (who is also a playable character), they are "missionaries," "the last resort" to "bring the Word of the Goddess to unbelievers."
In Xenosaga - Ormus is a religion with its own full-fledged military industrial complex, including weapons and advanced physics research.
The Aeon Illuminate of Supreme Commander has its military wing, led by the Avatar of War. Aeon ranks are known to include Knight, Templar, and Crusader, which should tell the player plenty. If not, their enormous robotic army, navy, and air force includes the Exodus, Harbinger, Fervor, Radiance, and the dreaded Galactic Colossus, termed the Sacred Assault Bot. Oh, and their nuclear missile launcher is called the Apocalypse, and they have a rapid fire artillery shotgun called the Salvation.
The Order of the Hammer, or Hammerites, from the Thief series. They often pray to their God to lend them strength to fight their version of evil (Pagans and anyone that doesn't think like them).
Paladins in World of Warcraft are always members of a militant religious order that varies by race. Human and Dwarf Paladins are Knights of the Silver Hand (originally the only Paladins in the game, and the terms were almost synonymous); Draenei are Vindicators; Blood Elves are Blood Knights; and Tauren are Sunwalkers. Priests count as well, though their agendas vary.
On an organizational level, there have been several Church Militants based around the Light. In order of their creation: The Order of the Silver Hand; the Scarlet Crusade; the Argent Dawn; and the Argent Crusade.
Hunter: The Reckoning had a priest. With a sword-slash-crucifix. And a crossbox-slash-crucifix. AND he could shoot light out of his hands. Proving that priests have secret magical powers that will be useful in the event of a secret zombie apocalypse.
Not sure about the video game, but in the table game from which it's derived, powers are granted for mysterious reasons to seemingly incongruous and unrelated people. Many characters, left with no rational explanation for their new powers, are going to explain them the best they can based on their cultural background. In other words, if a 'typical' American suddenly was able to sprout a flaming sword and smite a vampire with it, all the while hearing voices or seeing hidden messages, what's less likely than that they would attribute it to God? And if a priest gained such powers, religious mania is a perfectly reasonable outcome.
La Pucelle is about a squad of monster hunters belonging to a church whose (sorta secret) purpose is destroying demons.
The Church of Elemia from Ar tonelico: Melody of Elemia, as evidenced by Cardinal Radolf's really nice spear. This is because Bishop Falss formed them with the intent to invade Platina.
RuneScape: Priest robes (prayer bonus), best mace you can find (prayer bonus), hunt giants/dragons (their bones give more prayer xp). You can take a lot less damage (Protect from x prayers) while dealing a lot more damage (Fortify Strength/Attack/etc.) And, the Monks of Zamorak, too.
Halo has the Covenant, a conglomerate of alien species that embark on crusades in the name of their gods, the Forerunners, all in the name walking the path to the Great Journey.
The priest class of Dungeon Fighter Online is supposed to be a support class, albeit a support class that's NOT a frail caster that needs to run away when danger approaches. Those bulging muscles and that oversized weapon he carries on his back isn't just for show.
And now we have Toyosatomimi No Miko, another religion-inspired fighter (Taoism) who led a sort of crusade to make Buddhism the state religion in her country while secretly practicing Taoism. This backfired a lot, since when she tried to use Taoism to ressurect later on, Buddhist monks sealed her away.
An often-overlooked bits is that even Yuyuko and Youmu are Church Militant of a Buddhist esoteric order. Their stages are heavily based on the concept Pure Land, and their spellcards based on teachings of Buddhism (notably the aforementioned Pure Land esotericism).
RosenkreuzStilette has a variant on this: the titular group was formed after the hero Rosenkreuz and his eight closest disciples won a holy war against the Holy Empire, and became a Magi-specific order of the Orthodox Church's army. Unfortunately, the Church and the RKS seem to have come to blows again recently...
The Crusaders in Final Fantasy X, although they have the odd distinction of being officially excommunicated by the time the game starts for consorting with Al Bhed heretics and their machina.
The Warrior Monks of Yevon and, to a lesser extent, the Summoner Guardians, since they're respectively the army and the bodyguards of the "saints" of Yevon.
The Fire Emblem series tends to have quite a few of these about. Many of the backstories of the games will feature a group of badass heroes saving the continent, and at least one of them (Archbishop Blaggi, Saint Maira; Saint Elimine; Saint Latona) will count as this and as the founder of their own religion, which is then spread through the years and lands. Then, when the world's in danger, members of such churches will join the hero's armies to fill the trope and fight for it.
There are tons of examples in Dark Ageof Camelot, most notably the Cleric, Paladin, and Friar of the vaguely medieval Catholic church in Albion, and perhaps the best example in Midgard, where even the 'wizard' classes use piety instead of intelligence to determine their spell strength, and each class has its own Norse patron deity (For example: Odin for Runemasters, Hel for Spiritmasters, Thor for Thanes, and Loki for Shadowblades).
Dragon Age has the Templar order. They exist to carry out the Chantry's (church's) will using military might. They're trained to be skilled at fighting mages, in order to ensure that all mages in the chantry's territory (they intend to become the main religion of the world) are aligned with the chantry.
The Seekers of Truth, who answer solely to the Divine herself. They primary serve as a check and a balance to the Templar Order, working to investigate any signs of corruption or dissent within its ranks. Other Seekers work to protect the Chantry from threats, both external and internal.
On a character level, Leliana. While not an ordained member of the Chantry (she never got around to her vows), she's very open about her faith. Her skills were also learned in her life prior to finding religion, but she's not above using them in what she believes is a divinely directed mission to aid the Warden.
Following in a similar vein, Prince Sebastian Vael in Dragon Age II, an ordained brother in the Chantry who takes his faith very seriously. While he's mostly pacifistic, he's not above lending his bow to help curb the more criminal elements present in Kirkwall, as well as deal with rogue Mages. He slips towards the more militant side after Anders blows up the Chantry and kills the Grand Cleric. If Hawke does not execute Anders, Sebastian openly declares his intention to head to Starkaven and raise an army, then return and raze Kirkwall to the ground.
The Church of Zakarum from the Diablo series has the paladins, who were founded to protect the monks who were meant to spread the religion. For some reason, the kind, generous, armed knights were more inspiring to the populace than the monks. They faded from view once Zakarum no longer put a lot of effort into converting people, only to make a comeback when the Prime Evils started attacking the mortal world, and Zakarum decided to start converting again. This time, anyone inconvertible was deemed evil and killed. A small band, including any paladin player characters from Diablo II, chose to go rogue, and directly confront the Prime Evils. They later discovered that the church they served was corrupt, and had to face several enemies that were themselves examples of this trope.
An earlier offshoot of the Church of Zakarum, the Crusaders, make their return in the expansion to Diablo III. This order was originally formed two hundred years before the events of III, when the corruption within the Church was noticed by a high-ranking church official. The Crusaders are tasked with finding and eradicating the corruption within the Churchnote Even though the cause of the Church's corruption—the Prime Evil Mephisto—was slain by the heroes of Diablo II, they do not consider the quest ended.. The Crusaders had disappeared into the far eastern parts of the world and were initially thought lost for good, but their crusade—passed on from mentor to novice through the generations—eventually led them back into the western world.
Elsa la Conti and Clarice di Lanza of Arcana Heart, a pair of nuns who work for the Western Europe Spirit Sector. Elsa has a large cross used similar to a tonfa, as well as a gun, a whip, holy water, and other weapons for dealing with demons, spirits and the like. Clarice...doesn't need any of that stuff because she herself is a demon.
Septerra Core. The Holy Guard of the Seven Winds, an order of paladin-type fighters from Shell Three.
The Ikko-Ikki in Total War: Shogun 2. A Buddhist militant monastic order of commoner men who oppose the decadency of clan rules. They even have their own form of Buddhism, Jodo-Shinzu, which is incompatible (in game-mechanic way) with Shinto-Buddhism practiced by most of Japan. And they are Badass.
Any faction can have Warrior Monk units, which are some of the most expensive, hardest hitting, and deadliest units in the game (outside of hero units). Their only draw back is that their monk robes aren't very good at stopping arrows.
In Spore, during the Civilization Stage, if your nation has a religious inclination, you build tanks that utilize music instead of cannons, and laying seige to a city consists of getting your music tanks to play (while a holographic preacher shouts at the city walls).
Similarly, the game's Space Stage features a number of archetypes; one of which being the Zealot. Zealots are fanatically dedicated to Spode, and believe it is their duty to convert others to his worship, and smite all who refuse. The power given to players using this archetype is called "Fanatical Frenzy," allows you to instantly convert all cities on a planet, transferring it to your empire's control. However, due to the forcible conversion, any neighboring empires will treat it as a weapon of mass destruction and therefore will not trust anyone who makes use of it.
Civilization V: Gods and Kings has one religious belief called "holy warriors," which allows you to buy pre-industrial units with faith instead of gold or production. However, there is no gameplay of cosmetic differences between holy warriors or normal units.
In Fallout: New Vegas, the Mormons (now known as the New Canaanites) are a benevolent example. While they are known for being incredibly proficient in firearms (specifically the M1911 and the Thompson SMG) they are also known for generosity and offering help to anyone they can.
Medieval II Total War has this during Crusades called by the Pope. While you're on a Crusade, the Crusading army in question can recruit religious mercenaries that include fanatical pilgrims, spearmen, or cavalry. Outside of the Crusades you can recruit various knightly orders. There's also the Papal States, who sometimes will go into an expansionist phase and conquer various cities around Rome.
Madness Combat features a version of Jesus who fits this trope perfectly.
Sister Mona Theist of Flaky Pastry, as a member of the Sisters of Holy Retribution, fits to a tee.
The Vatican church of Cry Havoc employs teams of vampire and deamon hunters. They're preferred weapons are automatic air burst grenade launchers, broadswords, helicopter gunships and strike bombers. The only competing religion, the Norse based Aesir church, is implied to be even more aggressive with its methods.
Tech Infantry has the Christian Federation, one of several rebel factions during the Third Civil War. There are also Crusader Teams who hunt Vampires in the Federation, and later in the Middle Kingdom.
Open Blue features the Order of Saint Lennox, which is more or less the Avelian Church's Inquisition. Suffice to say, even after the inquisition, they teach their preists (and maybe even nuns) to use a sword or two... or three... or six... This is likely because the Order sends many of its priests off as chaplains on Avelian warships, and in a time of pirates, you can never be too careful. The Order of Saint Clara trains nuns to fight against black magic and The Legions of Hell.
In the Whateley Universe, Petra and the entire Order of the Rose and Thorn, who end up fighting a host of necromancers who are trying to raise an Eldritch Abomination. Things escalate, and we find out just how well armed they really are.
The five Cathedrals, in The Graystone Saga, each have their own in-house team of defending soldiers, which makes sense since the Cathedrals are also sort of like royal palaces. Lady Gray, the protagonist, is herself a church militant of some sort, and the presence of the other soldiers seems to have something to do with the fact that she exists.
The Hashishim, aka The Hashshashin, a heretical Ismaili Muslim cult organized by Hasan-i-Sabbah with the goal of overthrowing the Caliphate. They were said to use hashish to induce visions of paradise that the believer would obtain upon his death, though this is considered a myth (especially by the scholar Edward Burman), as the effects of hashish were well known in the Islamic world at the time and any such claims are a later misunderstanding of the sect. The word "assassin" derives from the name of this sect, and derives from Hasan-i-Sabbah's name rather than the word "hashish." Another theory is that the name is "Asasiyun", "those faithful to the foundations" (asa:s) of Islam.
One of many real, Older Than Print orders: The original Knights Templar (and several other crusading orders established thereafter) were originally intended to be an "order militant" of the Catholic church organized along monastic guidelines entrusted to protect and provide care for Christian pilgrims to the Holy Land. However, the Templars gradually grew in power, wealth, and influence to the point that they were largely autonomous of any overseers, whether religious or secular, until the King of France convinced the Pope (who was a virtual captive at Avignon, in French territory) to disband the order and brand them as heretics in 1314 (possibly because he owed them money).
The Knights of the Hospital of St. John (Hospitallers) were not affected by the dissolution of the Templars. They kept fighting from bases on Rhodes and then Malta until they were invaded by Napoleon in 1798. Since then, they have ceased their military activity. They do still, however, exist, and are recognized as a sovereign territory-less state. They even have a few citizens.
The Order of the Teutonic Knights of St. Mary's Hospital in Jerusalem (or Teutonic Knights) was both a monastic order charged with evangelization and christianisation of pagan teritories, mostly in the Baltic regions, as well as considerable military force and a sovereign Monastic State. They ended up turning themselves into secular nobles when they turned Lutheran, and their military state became Prussia.
From about 1378 to 1418, the Catholic Church fought a civil war. A real civil war. With actual battles and many, many factions.
The English city of York had some pretty tough Archbishops before the reformation. In 1138, Archbishop Thurstan formed an army at the Battle of the Standard and routed a Scottish army. In 1346, another Archbishop (the fantastically named William La Zouche) defeated a numerically superior Scots invasion at Neville's Cross near Durham. Yet another Archbishop, Richard le Scrope, led an unsuccessful uprising against King Henry IV in 1405. One of Henry VIII's Archbishops, Christopher Bainbridge, ended up going to Italy and besieging the city of Ferrara for the infamous "warrior Pope" Julius II. And this was just one See...
Thurstan didn't actually command the English at the Battle of the Standard (he was in his 70s at the time, pushing towards 80), but he did raise the force and created the famous "standard" - which consisted of the blessed sacrament mounted on a cart with the banners of St Peter (patron of York), St Wilfrid (patron of Ripon) and St John of Beverly (patron of... three guesses). The message to the Scots was clear: by fighting the English they would by virtue of the standard be fighting three saints and Jesus Christ himself. Thurstan's personal representative at the battle was fellow Bishop Radulf Novell, who delivered an inspiring sermon to the English before battle commenced and probably participated himself. All this appears to have had a profound psychological effect on the Scots, who went on to lose badly. Probably at no other point in British history has religion been used so explicitly as a weapon of war.
Another Archbishop of York to take up the sword was William Melton, albeit without much success. In 1319 a Scottish army threatened York, and in particular Queen Isabella of England who had taken up residence there. While the Queen was smuggled out of the city by boat, Archbishop Melton hastily raised a rather small, ragtag army of York residents, which involved a large number of priests and monks from the region. Unsurprisingly, in the ensuing "battle" at Myton-on-Swale they were massacred by the Scots. The sheer number of clergy and religious men involved on the English side led to the battle being nicknamed the "Chapter" of Myton.
Many modern militias in the Islamic world, for example Hezbollah, combine civil defense with religious education. Secretary-General Hasan Nasrallah was trained in Iran as a religious scholar. However, at least in Hezbollah's case the religious element takes a backseat to civil defense, and many Maronite Christians and Druze are members or supporters of Hezbollah. The Mujahideen and Taliban soldiers also ooze this trope, as do Al-Qaeda, Hamas, etc.
Some people accuse Islam to be a religion spread "by a sword in the left hand, and a Qur'an in the right hand". While it's not entirely true, they had reasons for this; their power and fervor is such that they were able to take out the Persians completely and fight toe-to-toe against the Eastern Roman Empire.
While the above is partly true (Islamic rule spread rapidly through a strong military force, while the actual conversion took sometimes centuries; see the Copts in Egypt)), this can be said for many religions, especially once a regionally dominant power starts to spread it in neighbouring countries, such as, say, the spread of Christianity to the Aztec Empire, parts of sub-Saharan Africa, and South and East Asia.
In medieval Korea (during the reign of Goryeo Dynasty), there were official army faction of buddhist monks, with badass sounding name of 'the army of Demon-repellers'('Hangmagun' in Korean), which fought against Jurchens and Mongolians. The succeeding Joseon Dynasty(which disliked Buddhism due to its Confucianistic nature) banned these 'Monk Armies'('Seung-byeong', which means the same as Japanese 'sohei'). But later during the 1592 Japanese Invasions, many Buddhist monks took up fighting again as Seung-byeong, and some famous monk-generals such as Samyeongdang contributed greatly in driving out the invading Japanese forces. Their names and feats were so well-known that there were many folk legends created about monks being able to use magic and supernatural powers.
In Feudal Japan, prior to the Tokugawas' consolidation of control, there were quite a few orders of warrior monks ("sohei"). Many of them were of samurai origins themselves (some were ronin, others preferred the religious orders to serving a secular lord) and all of them were just as tough customers, and as ferocious, as the samurai. There were full-scale wars between rival temples, and Tokugawa Ieyasu had to put them all down very hard to get the country to be quiet.
The Ikko-Ikki's description up in the Video Games section covers the basics, their beliefs made even their allies hate them. It took Oda Nobunaga three separate sieges to bring down their fortress at Nagashima. He didn't even manage to take it conventionally; the third siege ended when Oda forces managed to surround it and burn it to the ground, including numerous civilians and non-combatants within.
During the early 20th century, the Catholic Church and the post-revolution Mexican government came into conflict. The Constitution of 1917 had several articles in it that severely limited the power of the church in Mexico, although not all of these were immediately enforced. During the administration of President Plutarco Calles, the government began secularizing education, forcing priests to register with the government, and capping the number of priests in the country, and persecuting Catholics that resisted (violently or not). The Church wasn't pleased with this, and, after putting the entire Church in Mexico on strike, numerous supporters of the church rose up in arms, calling themselves the Cristeros. The conflict escalated to the point where in 1928, the Mexican government executed José Sánchez del Río, a fifteen-year-old boy who refused to renounce his faith.
The Jesuits (the Society of Jesus), one of the many orders of priests in the Catholic Church, were founded in 1534 by a Spanish ex-soldier named Ignatius of Loyola. Ignatius had been wounded in battle, and spent the next few years wandering around Spain as an ascetic. Ignatius then decided that he should go become a priest. While studying in Paris, he and six of his militant student-priest friends got together, called themselves the "Company of Jesus" (as in an infantry company), went to Rome, pledged their absolute loyalty to the Pope, and said "let us form an order of priests, and we'll do whatever you want." The title of the papal order that established the Jesuits? Regimini militantis Ecclesiae — "To the Government of the Church Militant." Even today, Jesuit priests take a "Fourth Vow" - in addition to the usual vows of poverty, chastity, and obedience that all Catholic priests make - to do whatever and go wherever the Pope commands them. (Ignatius wrote that he wanted the Jesuits to be "well-disciplined, like a corpse." He wasn't kidding.)
The fourth vow also involves not seeking personal advancement in the Church, and refusing offers of it unless they are absolutely forced to accept, since St. Ignatius really didn't like career clergy.
The more modern lay confraternity, Miles Jesu, actually means "Soldiers of Christ". The Jesuits have been noted to not appreciate the competition, and innumerable conspiracy theories involving the recent Papal investigations into the activities of Miles Jesu have been floated.
The more successful Opus Dei, ("Work of God"), has been able to score major inside positions with recent popes, due to the occasionally "overkill" methods of the Jesuits. The so-called "Black Pope" of the Jesuits (the Father Superior, actually) has been sidelined by the more recently successful Opus Dei counterpart, and time will tell if the Jesuits have truly chilled and outlived their efficacy or some major upset will happen to replace them to their previous position as the "soldiers of Christ".
Considering that the actual Pope (Francis) is the first Pope belonging to the Jesuits, it seems they may be not that far off.
Until the 1960's the Vatican State technically still had an army. And it had a real army until 1870 when the Kingdom of Italy invaded and annexed the Papal States.
To the Catholic Church itself, this has a very specifically defined meaning: The term "Church Militant" actually means "all living Catholics in communion with the Holy See." The other parts beings "Church Triumphant" all souls in heaven and "Church Suffering" all souls in Purgatory being made ready for heaven. "Church" here means the group of people who are believers, not the building or institution. In other words, all those still alive are fighting a spiritual war, but those who have died and gone to heaven are done with the struggle and have been made victorious by God.
New England Puritans actually stored gunpowder in their churches. This made wintertime rather difficult as they could not light a furnace.
When the congregation started to disturb the mood by shivering the preacher would shout, "STAND! And hear the word of God!" It is NOT an accident that Battle Hymn of the Republic was written by a New Englander. This is why the Parthenon in Athens is in ruins. The Turks used it as a mosque, and were also storing munitions there in 1687 when a Venetian artilleryman took a potshot at the building, with predictable results.
The British used to say that The American Revolution was "a Presbyterian war". Whatever the religious affiliations of the top brass, the American lower ranks quite often considered themselves a Church Militant.
One British regiment traditionally takes its arms to church with them and posts guards during service. This dates from the time when their regiment was in the service of Scottish Covenanters. According to Bryan Farwell, Highland regiments had a notable level of piety, especially as compared to other British regiments.
In Welsh regiments, soldiers are, to this day, more likely than not to sing hymns on march and not swear.
In a subversion, some of the most Orthodox of Israeli Jews are ambiguous about Israel in the first place and are sometimes accused of being slackers. This is not universal and a number of Badass Israelis are quite pious Jews. The Druze in Israel have actually requested to be subject to conscription.
The Salvation Army is commonly seen as a general Protestant charity. However, they are this trope: a church organized along military lines, although the denomination isn't devoted to warfare, but rather aggressively trying to end poverty and help their fellow man. In the youth of the organization, however, the Salvation Army fought a large number of street battles against rival gangs and mobs raised by people not to keen on their radical message.
The Mormon War. Joseph Smith Jr. was once the leader of the militia (especially noteworthy is Zion's Camp ) and also the prophet and leader of the LDS church. After Smith's assassination when Brigham Young was prophet and leader of the LDS church they organized the Mormon Battalion which is the only religious military unit in United States history and was part of the Mexican-American war.
Sikhism is famous for this aspect. They express it in a more publicly accepted fashion then some groups, through such means as participation in regular military units and the carrying of symbolic weapons. Defense of the righteous is fairly central to the faith of Sikhism, which is understandable considering their history of being surrounded by militant Islamic factions and equally militant Hindus. They represent only about 2% at most of the Indian population yet make up nearly 15% of the army (and 20% of officers). Indian UN peacekeepers are usually called blue turbans due to the high probability they're Sikh soldiers (most male Sikhs do not cut their hair and keep it in a turban).
According to Robert Graves in his autobiography Goodbye to All That, during World War I British soldiers preferred Roman Catholic chaplains because not only did they actually visit the men in the trenches but when other officers were killed they would take off their chaplain's tabs and lead the men themselves.