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- The Belkan Church of the Saint King in the Lyrical Nanoha devotes it resources to building schools and hospitals and provides assistance to the Time-Space Administration Bureau whenever they can. In the third season, the Bureau itself (for whom all of the protagonists work) has been revealed to have a darker side, so the Saint Church remains as the only incorruptible authority in the setting.
- Trinity Blood has The Protagonist Abel Nightroad as a friendly and goofy fellow. The head of the church is also a Nice Guy. Other members of the church are less heroic.
- Mahou Sensei Negima! has a church-related arc, wherein the clergy are supposed to be of the "kindly old man" variety, even though we never do meet them. The local nuns are, in fact, mages in nun habits.
- in the Hellboy comics, the church, and holy men in general are generally portrayed positively. Most priests are pretty nice guys and their blessings are genuinely effective against minor demons, though big ones like Helldad can shrug them off. Even vicious ones like the Inquisitors from The Island and the Witchfinder General were usually the lesser of two evils. The Mignolaverse's cosmology is based in early Celtic mythology, corresponding to the time where the churches of the white Christ were around, but not necessarily dominant.
- For the most part, the Catholic Church in Warrior Nun Areala is portrayed very positively, as being an organization working directly under the authority of Heaven, empowered to hunt down and battle the forces of Hell, and optionally more mundane villainy such as Nazi masterminds. The order of Warrior Nuns is armed with weapons that, while lethal to demons and the undead, do not harm humans.
- In Marvel's What If?... story where Wolverine became the Horseman of War future is an wannabe-utopia where humanity has united under the threat of War (as in Wolverine, not war). There are retreats, held by monks, for people who wish to practice peace more than the other people. The monks are the ultimate keepers of peace, teaching the way on non-violence in a world without war. One of the monks is Brother Xavier, who really is Wolverine, who has learned how to keep his anger in control.
- The Blind Side: Christian charity is part of what motivates the Tuohys to help Michael.
- Star Wars: The Jedi are like monks with lasers swords. They catch criminals and mediate conflicts.
- Jesus Christ Vampire Hunter: Naturally, when Christ Himself is out smiting evil He's going to have some disciples doing likewise.
- In The Minion Dolph Lundgren is a warrior priest who is a member of The Knights Templar. They hunt demons with blessed holy gauntlets fitted with spikes.
- In the biopic of Pope John Paul II, for obvious reasons.
- In Of Gods And Men'', the French monks caught up in the Algerian civil war are like this. They've provided medical care and social services to their Muslim neighbors for decades, and are shown studying the Qu'ran. When Islamist insurgents try to kidnap the doctor at gunpoint, the abbot insists that if they bring their injured comrades to the monastery, the doctor will provide care no questions asked. The monks are as good as their word. When an opportunity to flee the violence arises, they all refuse because the villagers need them and, after all, Jesus wouldn't run from violence. They all get kidnapped and executed.
- The Universal Church in Alan Dean Foster's Commonwealth books is one of these.
- Almost all of the religious organizations in The Dresden Files. This series runs on All Myths Are True and Fantasy Kitchen Sink, so there has to be a benevolent god who acts through saints, priests, and knights. This isn't necessarily the same thing as the entire institution being benevolent, it's just that Harry specializes in dealing with the magical bits of the world, and the magical bits of Catholicism are based in the mythology of absolute goodness. The priests in the church that don't have the power of faith and so on just don't show up in Harry's baliwick. Most specifically St. Mary of the Angels in Chicago where Father Forthill resides, but there's also the Buddhist monastery that Mouse the Lion Dog puppy came from.
- The churches run free hospitals in Jennifer Government, where everything down to the ambulance service is privatised. Volunteers for the hospitals take the hospitals name as a auxiliary surname.
- The Christian Church in Quo Vadis? is unambiguously good. Its members live simple, happy lives, standing above the depraved environment surrounding them in Ancient Rome.
- In the backstory to HP Lovecraft's The Haunter of the Dark, the evil Nyarlathotep-worshiping cult are routed by a Catholic/Baptist alliance between Father O'Malley and the Reverend Drowne. At the climax of the story, a group of Italian Catholics attempt to contain the avatar of Nyarlathotep within its prison using candles, but, sadly, it slips through.
- David Weber's Safehold books has the Church of Charis, created in book two in response to the corrupt Church of God Awaiting, headed by Archbishop Maikel Staynair.
- From the Honor Harrington series, most religions are implied to be this, including Second Reformation Catholic (Queen Elizabeth III), Third Stellar (Honor herself) and the Church of Humanity Unchained (Grayson edition), which, although highly conservative and somewhat sexist, is largely good - personified in leader Reverend Hanks. Obviously, the Masadan variant - well, not so much.
- The Universal Brotherhood in E.C. Tubb's "Dumarest" books. The "monks" are pacifistic, doing good among the downtrodden, oppose the machinations of the Cyclan, and frequently assist Dumarest against them.
- The Omnian religion in Discworld, once Brutha becomes Cenobiarch at the end of Small Gods.
- The Catholic Church in A Canticle for Leibowitz is portrayed as being the sole retainer of knowledge from the times before the Fire Deluge.
- In the Lord Darcy series, the Church polices both itself and the Empire's sorcerers, using magically-Talented Sensitives to check that its members remain free of corruption.
- Song at Dawn is said to be led by a "genuine innocent" (Innocent III) and the church in Nabornne is only antagonistic to the heroes because its arch bishop has a personal grudge against one of them. The rank and file members are genuinely zealous about reclaiming the Holy Land, preaching self-discipline, and steer clear of Knight Templar territory.
- In Poul Anderson's "The Live Coward", the abbot is a shrewd politican. Nevertheless, Wing Alak knows better than to offer a direct bribe. When the abbot does ask for return, it's for technical expertise to advance farming on his planet — and for himself, some books on astronomy translated into their language, asked for with such touching curiosity about the stars that Alak resolves to keep it, though his job calls for him to break such promises without mercy.
- Kindling Ashes: The Temple of Lua and Soan is a complicated example. They provide Giselle a bath and a warm meal just for showing up and looking like she needed it, but also because she wants to become an initiate. She's there on a gold smugging assignment because no one would think to look for a hidden cache there, but Giselle thinks that this means that part of the clergy is part of the operation. She generally has a poor opinion of them because they thinks she's possessed, and she is, but by a dragon instead of an evil spirit but the clergy of this region isn't likely to see a difference because of the recent dragon war.
- Journey to Chaos:
- The Priesthood of Zaticana spend their time volunteering as translators, starting summer reading programs and running the public library.
- The Brotherhood of Death work as hospices and also police in the case of necrocraft crimes.
Live Action TV
- The Way of the Prophets in Star Trek: Deep Space Nine. Granted, for most of the series its leader is Sinister Minister Kai Winn, but it's made clear that she doesn't really have that much influence on what the church itself believes, and her subordinates continue to be Good Shepherds.
- The nuns of Nonnatus House on Call the Midwife exemplify this trope, always caring for their poverty-stricken patients while refusing to pass judgment on them, to the point where the show may very well contain the most positive portrayal of Christianity of the past decade.
- Doctor Who:
- On "New Earth" the Sisterhood run a hospital founded by charity to heal the sick. They take oaths to do nothing but heal the sick. One of them says that the 'people farm' thing was a last resort because nothing else they tried worked fast enough to heal all the sick people coming to them. When Cassandra releases the clone-humans, they quarantine the hospital to prevent anyone else from getting sick. They are still in the hospital when this happens.
- "The Time of the Angels" introduces a militarized church from the 51st century. It provides heroic soldiers that help the Doctor neutralize the Weeping Angels. Octavian gives the sense that this is a routine mission. They're even helping criminals atone for their crimes (albeit in the sense of a parole officer).
- The Church of Pelor... and every church of good aligned deities in Dungeons & Dragons that are on the ball.
- Other major examples in the Third Edition standard cosmology are Hieronious, Kord, Moradin, Corellon Larethiean, Garl Glittergold, Yondala, and Bahumat.
- In the Forgotten Realms setting, Ilmater tends to be this especially, but then, he is Crystal Dragon Jesus more than most. Also the divinely-granted spells of the worshipers of Sune, Goddess of Beauty and Love, are the closest thing to weaponized love in the setting.
- A good Eberron example is the ancestor-worship of the Elves of Aerenal, which is Neutral Good and splits its time equally between giving advice to the still-living Elves and beating seven shades of undead crap out of the Blood of Vol.
- The Ministry of Elemental Good.
- The Dragonlance setting has the Church of Paladine, which had become a Corrupt Church by the times of the Cataclysm, but, reborn under the guidance of Elistan, now fits the bill.
- In short, almost any church to a Good deity will either have extensive charitable operations or a generally benevolent police force, if not both.
- The Church of Sigmar in Warhammer Fantasy, except for the Witch Hunters, of course. Even the good ones are pretty vicious.
- Also Temple of Shallya, goddess of healing and mercy. And non-violence, what is quite hard a commitment in such a violent world as Warhammer. Church of Sigmar is the good guys, but it's more an example of Lawful Good Church Militant.
- The Brotherhood from Mutant Chronicles. Soulsaving Crusaders to a man, and willing to torture suspected heretics and assassinate dissidents. They also run charitable hospitals, schools and soup kitchens, maintain the only universally recognized bank and currency, and mediate in corporate disputes.
- In Magic The Gathering, The Church of Avacyn on the plane of Innistrad is the only shining beacon of hope for humanity in a plane full of many horrors, most of them undead in one way or another. The church employs various Catholic-esque imagery, such as the Mark of Avacyn, a vaguely cross-like symbol used in many of the same contexts, and naming its prominent members as "Saints" (during life rather than posthumously). Unfortunately, its patron angel Avacyn is AWOL— until Avacyn Restored, where she breaks out of the Helvault to restore the Balance Between Good and Evil.
- The Churches of the unnamed deity in the Dragon Quest series.
- The temples of the Nine Divine in The Elder Scrolls are uniformly benevolent. It contrasts against the mostly evil Daedric cults, though the Daedra themselves operate on a very Blue and Orange Morality.
- Several standalone churches in Fallout3. The player can donate to them to increase their karma.
- Even the ones that get people killed are well meaning and misguided (and you can make them realise the error in their ways)
- The Mormons, now called "New Cannanites" over at New Vegas.
- The Light of Kiltia in Final Fantasy XII. Benevolent, politically-neutral (their priests are forbidden to engage in matters of the state), and deeply protective of refugees and pilgrims. It is implied, however, that in the mythology it shares with Final Fantasy Tactics and Vagrant Story its diminished political power allowed the Church of Glabados and the Müllenkamp cult to appear from within its ranks.
- Danette's parents were part of one of these in Soul Nomad & the World Eaters. One was a priest, the other a mage. Revya's group also protects one of these from Thurists.
- The Church of the Holy Light in Warcraft 'verse. Their offshoot, the Scarlet Crusade, is less so. Disgruntled members of the Scarlet Crusade also have their own reformist organization, the Argent Dawn, which is an equal-opportunity employer and even has high-ranking undead members.
- The various Churches of Mana from the World of Mana series.
- The church of Nisan in Xenogears, led by Sophia as its Holy Mother.
- The Church in Palm Brinks in Dark Chronicle. It's sole purpose is to allow you to recruit Priest Bruno and let you get a few photos for the photogrophy mini-game.
- The Zedem church in Startopia is old-fashioned and moralistic but seems genuinely well-intentioned, spreading the word by evangelism and its adherents being nonviolent ascetics. Much more importantly, they pay the administrator a lot of moolah if you let them set up a church on your biodeck and bring in converts — a more high-risk, high-reward alternative to more secular alternatives of dealing with sinners.
- The Church of the Holy Maiden in La Pucelle; although the game actually questions the notion of faith in gods at some points (and even their goddess, Poitreene, herself claims not to be perfect at one point ) the Church is still largely a force for good that cares for the people. On the other hand their rivals, The Church of the Holy Mother, turns out to be a Religion of Evil in disguise but has more worshipers.
- The monk and his church in King's Quest II help Graham a great deal. The Fan Remake? Not so much...
- Shining in the Darkness has a church where you can save your game.
- The Temple of Palfina in Hexyz Force. When they learn that Cecilia inherits Palfina's power, they throw all their support behind her despite her reputation as a slacker.
- The temples (which seems to be an expy of the Catholic Church) in Dokapon Kingdom cures you of your status ailments and serves as a checkpoint.
- In the Lufia series, churches serve as save points, and also have other functions such as teaching magic to party members.
- The Chantry of the Dragon Age series tries to be this, it honestly does. Unfortunately history has shown us that it is also self-important, intolerant, and extremely brutal in many of its methods, not to mention that on several occasions it has removed verses from the Chant of Light (their version of a holy book) in order to suit their political aims.
- The Church of the Harvest Goddess in the Harvest Moon series. They're typically run by a kindly minister who will always listen to your troubles, even though you can often talk to the Harvest Goddess for yourself and see how she's doing. In the games set in Mineral Town (Back to Nature and For Girl, and the Friends of Mineral Town games), the church is a vital place where you can raise your friendship with the townspeople by confessing your sins, get cursed tools blessed to make them usable, and even get rare mushrooms from the pastor, who likes to garden a bit. In the Wii games (Tree of Tranquility/Animal Parade), it plays host to several festivals, and you can use it in Animal Parade to pray for the wishes of the townspeople to come true.
- The Hunchback of Notre Dame added a benevolent bishop character to offset Sinister Minister Frollo. The nice cleric got Frollo's job from the novel, that of Archdeacon.
- The Air Nomads in Avatar The Last Airbender are heavily implied to have been a Buddhist-inspired variation of this, mostly according to the backstory and a lot of Word Of God. They used all the money they made to support others, they fought only in self-defense, and the last surviving Air Nomad, the eponymous Last Airbender, makes reference to various Air Nomad wisdom from time to time. It's notable that as a whole, they were so spiritual that their entire culture could Airbend, while in the other Nations only a certain percentage can, though this may be related to their small population.
- This is so much a part of airbender culture that in one late episode, when Aang is conferring with his past incarnations to try and find a relatively peaceable solution to the problem of Fire Lord Ozai, he has a Heroic BSOD when the previous Air Nomad, Avatar Yangchen, admits killing Ozai as the best solution available to Aang. When a method to deal with Ozai without killing him presents itself, Aang takes it without question, even though he's risking his soul to do so.
Go now my child, and sin no more!