"Hence Theocracy is the worst of all governments. If we must have a tyrant, a robber baron is far better than an inquisitor. The baron's cruelty may sometimes sleep, his cupidity at some point may be sated; and since he dimly knows he is doing wrong he may possibly repent. But the inquisitor who mistakes his own cruelty and lust of power and fear for the voice of Heaven will torment us infinitely more because he torments us with the approval of his own conscience and his better impulses appear to him as temptations."
"His natural prejudices assumed the priesthood to fall into a small number of categories: old, mad, dissolute, fanatical or a delightful combination of any of them."
- – Roboute Guilliman's high opinion of Imperial priests.
"Thought for the day: blind faith is a just cause."
The Adeptus Ministorum, or Ecclesiarchy, is the state church of the Imperium of Man and works with the Inquisition, making it the group which defines heresy. The name is derived from the Greek Ecclesia, literally meaning Church but more generally "gathering" or "society".
When the Emperor of Mankind began setting up the Imperium, he began instituting the Imperial Truth, which basically said "there are no gods and we're doing materialism and rationalism now" to starve the Chaos Gods of power from human worship. Yet even during the Great Crusade people began worshiping the Emperor as a "God-Emperor", including his own son Lorgar, who wrote the Lectitio Divinatus. Which, ironically, proved effective at causing pain to demons when lines from it were spoken to them (since the Emperor had it backwards; faith and religion didn't give the Chaos Gods power, faith and religion towards other things besides Chaos actually starved Chaos of power). Suitably embarrassed, the Emperor politely informed Lorgar to stop that... by having the Ultramarines destroy a city the Word Bearers set up and then forcing Lorgar to bow down to Himself, Malcador the Sigillite, and Roboute Guilliman in front of his legion. In an unfathomable and completely-impossible-to-predict act of Heresy, this would lead to Lorgar worshiping the Chaos Gods and starting the Horus Heresy.
And Rawbutt Girlyman is back, and he does not like the Ecclesiarchy (though it's their fundamentalism and fondness of luxury that Guilliman has issues with, not so much theism and religion itself; note his permissiveness of the Adeptus Mechanicus and Omnissiah, and his alliance with the Ynnari, agents and an avatar of the Eldar god of death). However the words of Cawl, Celestine and several others have convinced him of its necessity to the Imperium in its current state.
The Church Itself
The Ecclesiarchy itself is, officially at least, the one true faith of the God-Emperor. It is the organization dedicated to teaching His truths and His will to the vast masses of humanity, and all are united under its banner. Therefore, no matter where you go the Imperium, the Cult of The Emperor can be found uniting its masses under His benevolent rule. The reality, of course, is a bit more complex. The problem is that the Imperium is vast. Like, really vast. So much so that no one really knows how big it is, and an empire that big couldn't even begin to manage a galaxy wide faith. Therefore, what actually happens is that the Church of the God-Emperor is split into many faiths that don't actually resemble each other in any way.
On some worlds, the Emperor is worshiped as a distant father, watching over his children from far away. Others associate Him with a force of nature, believing that the wind is His voice and when He is angry He shouts at them causing great winds. Others assign some sort of totem animal, usually a predatory bird, that is considered sacred in His eyes. Some practice hymns and chants that wouldn't be out of place in our modern age, others prefer ritualistic dances and animal sacrifices. Despite all this varied and at times bizarre forms of faith, one thing is certain; there is only one god, only one Emperor, and they are one and the same.
The Ecclesiarchy attempts to promote and maintain the Cult of The Emperor wherever it can, if it is possible, to shape the local faith into something a bit more orthodox. As such, any planet with an Ecclesiarchal presence will eventually begin to resemble other faiths. Chapels will be built, a hierarchy of priests will emerge (what that hierarchy or even the priests will look like is a different thing altogether), and more extreme or shocking practices slowly weeded out or shaped into different forms. Even human sacrifice is re-purposed for the Emperor's benefit, as a culture that practices such things is much more willing to give up psykers to the Black Ships. It also helps that the Ecclesiarchy is willing to take the very slow, very long conversion route and accept even remote or vague Emperor worship under different names (such as Fenris's Allfather view of Him) so long as they follow a few basic rules. Very much like how the Imperium itself is structured, really.
Ironically, this makes the Ecclesiarchy oddly tolerant and open minded as they travel across worlds. They are trained to see past the individual beliefs to examine the core of the faiths they encounter, and therefore are unexpectedly tolerant of opposing sects, where more close minded citizens would be quick to denounce them as heretics and traitors. After all, the Emperor is a wise and benevolent god who loves all his subjects regardless of who they are, and the Ecclesiarchy follows His example. Seeing as the average citizen does not view other forms of Emperor-worship as heretical or blasphemous, someone must be at least somewhat educating them on the idea that any form of Emperor worship is acceptable if the Ecclesiarchy (*cough*Inquisition*cough*) approves of it and so should they or else they're the dirty heretic and will be "corrected", although this doesn't stop religious civil wars from being waged on occasion which nicely explains why Sisters of Battle might be fighting other Sisters of Battle.
The one area the Ecclesiarchy tends to butt heads is with the Adeptus Mechanicus. On the surface, the Cult of the Machine God runs completely counter to worship of the God-Emperor, especially since the Mechanicus' religion predates the Imperial Cult (and the Imperium itself) by a few millenia. However, there is little that the Ecclesiarchy can do about it, since 1. The Treaty of Mars guarantees not only autonomy, but religious exemption to the Mechanicus, and 2. Pissing off the Mechanicus is a bad idea since they control all the ships and tech. Because going to war with half of the Imperium would be monumentally stupid, they came up with a compromise that the Emperor is the physical avatar of the Machine God, bringing the Mechanicus closer in line to the Imperial Cult. This compromise isn't very satisfying for the more extreme fanatics, which can and does form conflict between the institutions beyond the political strife of two powerful organizations arguing over jurisdiction.
Less tense are the relations between the Ecclesiarchy and the Adeptus Astartes; Most Space Marines, the Black Templars excluded, do not officially embrace the Imperial Cult, having followed the older Imperial Truth that the Cult eventually supplanted. Instead most view the Emperor as a father figure than as a God. The Ecclesiarchy allows this since, in a manner of speaking, it's true that the Emperor is their father and they're not stupid enough to start a holy war against one of the most powerful military assets the Imperium has to offer; not to mention that few priests have the sheer balls to argue faith with a ten foot tall giant in heavy armor, although anyone else who denies the divinity of the Emperor is fair game. Well, that and claiming that the Emperor's own Angels can't view him as a man and not a god would be blatant heresy so their own followers would rip them to shreds with their bare-hands. Still, as a show of good faith, the Ecclesiarchy presents Rosariuses to Chaplains to demonstrate the supposed relationship between the Imperial Cult and the ancient spiritual traditions of the Astartes. The only exemption are the Iron Fathers of the Iron Hands, who worship the Machine God of the Mechanicus instead, something that bitterly annoys the Ecclesiarchy.
Age of Apostasy
After the Emprah was hooked up to the Golden Throne, a "Cult of the Savior Emperor" (more often referred to as the "Imperial Cult", since every Imperial's a member) was set up and eventually became the state religion as the Adeptus Ministorum, declaring the Emperor's very own Imperial Truth as Heresy. Well, more like claiming that the Emperor was trying to protect them through encouraging their ignorance of daemons. After all, declaring the Emperor's laws to be heresy would not go over well with the Astartes and Custodes.
The Ecclesiarchy was able to seize real political power in the wake of the Nova Terra Interregnum; after secular politics failed to reunite the twin empires of the Imperium, the Imperial Cult was able to leverage the widespread religious belief in the Emperor to bring Nova Terra back into the fold. However, this did not go smoothly; the Cataclysm of Souls resulted in vast amounts of bloodshed for anyone who rejected the Imperial Cult. This paved the way for the Age of Apostasy, when rival factions within the Imperial Cult battled for control of the church.
The Ecclesiarch, the head of the Ministorum, eventually got on the High Lords of Terra, eventually supplanting the Master of the Administratum (the guy who actually runs the government) as head of the Council. To show just how much power they could wield, the Ecclesiarchy moved from Terra to Ophelia VII at great expense, leaving Terra to rot, then moved back once they felt that they made their point. Hilariously, this mirrors a similar period of time when the Pope moved the Holy See from Rome to Avignon and later moved it back in a clusterfuck which for complex reasons ultimately culminated in three different people claiming to be Pope at the same time.
After that, the Ecclesiarchy did what every powerful group does: become more interested in its own power than the people they're supposed to be ministering, and public funds and taxes ended up funneling their way into the church, religious officials were making decisions on national policy and the like, since the Ecclesiarchy figured that the church and the state should be pretty much the same thing. The Ecclesiarchy also had a standing army called the Frateris Templar which stood apart from the Imperial Guard, but was presumably bad-ass considering how wealthy the church was at the time.
Reign of Blood
Things took a major turn for the worse when Goge Vandire, the Master of the Administratum, became Ecclesiarch at the same time, making himself the single most powerful person in the Imperium and started the Reign of Blood. Even by 40k standards this guy was nutters: He convinced an all-female sect called the "Daughters of the Emperor" (No,not them...) to rename themselves the "Brides of the Emperor" and become his bodyguards, they were also given the "finest weapons and armour" that the Administratum and the Ecclesiarchy could provide, which probably meant they were far better equipped than the later Sisters of Battle ever were.
He also instituted big brother policies of having Servo-skulls on every street corner listening for sedition, and engaged in mass executions/pillaging for the lulz, such as virus bombing planets, enslaving all female civilians of certain planets below the age of 12, melting polar ice caps etc, all the while claiming that he heard the voice of the Emperor himself.
A "rogue" preacher named Sebastian Thor and his "heretical" sect (the Confederation of Light), supported by a couple Space Marine Chapters and the Adeptus Mechanicus, went "fuck this" and invaded Terra to remove Vandire from the throne (so to speak). To the surprise of all present (except the Brides/Daughters), the defenders not only held off the invaders, but actually managed to give them a real beating. Before things got out of hand, the Adeptus Custodes took the leader of the Daughters to the Golden Throne to have a chat with the Emperor. She got insanely pissed off by something that happened there and cut off Vandire's head.
Afterwards, Thor didn't actually sit still and started travelling the Imperium to put things back together again and preaching the Emperor's good name. Once Terra had recovered, they had only one person in mind for the job of Ecclesiarch: Thor, but he refused to come back until the Imperium declared him a traitor and sent an army to collect him.
Back at the Imperial Palace, the Captain of the Custodes took him aside for a quiet word, and told him that he should either take the job or end up vanished. Thus, as the newly appointed Ecclesiarch, Thor started the Thorian Reformation, in which the Temple of the Saviour Emperor was supplanted by Thor's Confederation of Light. The Ecclesiarchy was stripped of all military power and the Frateris Templar had their funding cut and were reduced to the Frateris Militia which were not allowed to be paid or trained under the Ecclesiarchy's budget, but, fortunately for them, since they were specifically banned from keeping "men under arms", they reformed the Daughters into the Battle Sisters of the Adepta Sororitas.
The Inquisition also set up the Ordo Hereticus to make sure no one deviated from these new rules. The reformed Ecclesiarchy is only slightly less corrupt and divorced from reality as it was before, but now they feel guilty and beat themselves (and, unfortunately, everyone they minister to, which means every subjects of the Imperium) up about it! Occasionally, they even try (and fail) to fix it!
Sadly, some people are still particularly abusive, and these people are accused of having a "temple tendency." Additionally, there's an actual heretic group called the Temple Tendency. They believe the Confederation of Light are the real traitors and (secretly) preach their creed in the hopes of turning back the clock. They employ preachers known as Vandiran Apostates, or Shade Priests, which is a much cooler name than "Confessor."
At the top of the organisation is the Ecclesiarch himself, who is essentially the Space Pope and the equal-second (after the Master of the Administratum and along with the Fabricator-General of Mars) most influential individual in the entire Imperium.
Beneath him are the Cardinals of the Holy Synod. Although there are Cardinals all over the Imperium, each ruling their own Diocese (which is the religious equivalent to a sector in terms of size, but not organised the same way) the Holy Synod of Terra has a conclave of Cardinals who assist the Ecclesiarch in making religious decisions. Also, occasionally one of the members of the Holy Synod gets a seat on the High Lords of Terra, which is essentially giving the Ecclesiarchy more influence in Imperial affairs (particularly if the Abbess of the Adepta Sororitas gets a seat at the same time)
Beneath the Cardinals it moves downwards through the varying ranks of preachers, clerics, bishops, vicars, abbots, ministers, confessors all the way down to the the guys who light candles at shrines.
Aside from everyday priesthood there are a number of spin-off organisations that operate under the auspices of the Ecclesiarchy in one way or another.
While the sisters of battle represent the military might of the Ecclesiarchy the other orders of the sororitas also play highly influential roles for the church.
The Order Dialogus keeps the records and curates the relics of the Ecclesiarchy and are some of the most well educated and respected people in the entire Imperium when it comes to researching histories, languages or customs.
While the Schola Progenium trains generations of orphans to become "ideal" Imperial citizens, the Order Famulous get the job of "attending" the next generation of the Imperial elite. Teaching and educating key figures in Imperial nobility, these individuals grow up to be some of the most devout followers of the Imperial Creed and inevitably strong supporters of the Ecclesiarchy.
While the military might of the Ecclesiarchy was heavily curtailed by the Decree Passive that hasn't actually stopped them from summoning huge amounts of manpower when they need it.
All a cardinal needs to do is point somewhere and say the word "!CRUSADE!," and inevitably people will show up voluntarily in their millions. Most of them will be untrained and ill-equipped, but when it comes to manpower, the Ecclesiarchy can usually rely upon numbers to rival that of the Imperial Guard.
Games Workshop actually used to have rules for the Frateris Militia waaaay back in the 2nd edition Sisters of Battle Codex, but they vanished inexplicably, and reappeared briefly as a Troops choice for Codex: Witchhunters in a White Dwarf trial rules article under the name "Zealots", which could equally have represented Redemptionists as well as the Frateris.
They haven't been forgotten though, and FFG published rules for playing one in Dark Heresy, which is a decent way of giving more non-combat oriented careers the basic training in weapons and a few combat talents far earlier than they could have otherwise obtained.
A breach of the Decree Passive, Crusaders are professionally trained warrior-monks, equipped with specialist wargear.
Crusaders are trained in secretive warrior-lodges that are not directly associated with the Ecclesiarchy at all. According to the Codex: Adepta Sororitas the Crusaders associated with the Ministorum are recruited from the "Guard of the Cardinals Crimson". However, this may be a front, as many Crusader Houses are sponsored by the Inquisition, though it is uncertain if the Ecclesiarchy itself actually knows about that. For its part, the Inquisition deliberately allows the Ecclesiarchy to possess Crusaders in small numbers - there are all manner of uses for having a provable crime always ready to hand that the Ecclesiarchy is guilty of.
Membership is by invitation-only, chosen from those who will make ideal hand-to-hand warriors. Within the house they are deeply immersed in the Imperial Creed and are trained to be perfect bodyguards, putting the well-being of their holy charges ahead of themselves.
Whenever a traveling priest (or sometimes an Inquisitor) wants a little more protection, they can form up an Ecclesiarchy Battle Conclave. Because they can't have too many men due to the Decree passive, many opt instead to go with the scariest, most righteously out-of-their-mind fanatics they can find. Mostly formed from Arco-flagellants, Crusaders, and Death Cult Assassins, this terrifying force would make anyone think twice about fucking with him.
Not all of the priests tend shrines or preach at mass. One of the most well known functions of the Ecclesiarchy is bringing religion to the heathen humans beyond the territories of the Imperium.
Most of the missionaries accompany the Imperial Guard as they expand outwards, conquering or reconquering worlds, making certain that those who rebuild afterwards become loyal subjects of the Imperium.
Some Missionaries take it a bit further and don't even travel with Imperial Guard regiments, instead preferring to travel alone to hostile human worlds and bringing the light of the Emperor to them in more peaceful ways. These Torchbearers are expert survivalists and considerably more resilient than normal Ministorum Priests, having to live and prosper without any back-up at all.
Oddly, Missionaries tend to be some of the most tolerant and even tempered parts of the Ecclesiarchy even if their faith is beyond question and reproach and missionary lore as a whole is rather devoid of the usual grimdark and is instead...actually a really reasonable approach? As the Ecclesiarchy regards enforcing a single, consistent central dogma pure of any syncretic elements to be far too hard to do for too little reward in a rare example of common sense, Missionaries are instead expected to work with the heathens they want to convert and ease them into their new faith. Indeed overall the Imperium is far more tolerant of heathens then heretics and generally prefers an unusually soft and diplomatic approach to dealing with the former.
After all, a heretic or apostate is someone who knowingly flouts or abandons a faith like the Imperial Creed, but heathens by definition were never part of the faith to begin with; and so have a measure of innocence, especially if their heathenry was born of ignorance. And as part of this innocence and recognising the impossibility of enforcing a strict and singular dogma, the Missionary usually tries to modify the local faith into something more compatible with the Imperial Creed rather than tear their religion down and start from scratch.
In moves that are directly inspired by real world conversion efforts by monotheistic faiths throughout history, missionaries will look for the god or goddess held in the highest esteem by the local culture and then identify them with the Emperor. The other gods will then be equivocated to either aspects of the Emperor or to the most similar Imperial Saint in the canon depending on what works best. Often the Missionary will even study the theology of the local culture so in depth that they'll successfully argue that the Imperial Creed is a truer interpretation of the religion than what the established authorities are preaching.
They also try to preserve most local traditions as much as they can in order to make converting an easier sell with a few exceptions, which are usually traditions we in the modern world would find abhorrent like say; ritual rape or eating people. Cannibalism for example is strictly forbidden by the Imperial Creed
except when Space Marines eat people's brains apparently and so missionaries usually try to abolish such traditions and replace them with more symbolic eating of flesh and blood like how at the catholic church the "body and blood of christ" you eat at mass is just bread and wine that stands in for eating the poor bastard of a carpenter. They do however, try to change attitudes towards psykers and mutants to be more in line with official policy; psykers should be compliant servants who will willingly accept being taken by the black ships to serve humanity in some way, not kings and lords ruling over normal humans and unstable mutants need to be culled.
Whether the missionary works from the top down by converting the powers that be who will then enforce the imperial creed on the plebs or from the bottom up by converting the masses who will rise up against their heathen overlords and create a new society depends on the missionary's preferences and what they feel is easiest. As bringing new souls and cultures into the Emperor's light is holy work, just about all strategies are allowed in the name of saving the souls of heathens from the dangers of their ignorance.
As missionaries usually want converts, not corpses; use of force is generally a last resort and even then it's usually said force is used non-violently like having a rogue trader's ship eclipse the sun over their location to spook the primitives or show off the power of the imperial guard. The main exception to this is when the local religion is found to be based around xenos, abominable intelligence, or chaos worship. At this point the missionary's expected task is to call in the guard, sisters, or some other available military force to crack some skulls.
Confessors & Witch Finders
Like the Inquisition, the Ecclesiarchy concerns itself with rooting out heresy and apostasy. Unfortunately for the Ecclesiarchy it is not officially sanctioned to do so by the Imperium. However that has not stopped the ministorum from trying.
Confessors are loud, bombastic and charismatic priests of the Imperial Cult, but are not given specific duties like most members of the priesthood. Instead they are given carte blanche to travel freely from settlement to settlement and "cleanse" them of their sins. Typically by performing rousing soapbox rants about how wicked thoughts make the
baby Jesus EMPEROR cry. So people are encouraged to come forward to confess their sins to the confessor where he can decide an appropriate penance for them to clear their consciences. Confessors can be like the 40k equivalent of celebrities, and there is often great anticipation of their arrival in town, and big crowds show up to hear them preach (and probably hear their neighbours salacious confessions too). Sometimes people don't want (or have sins) to confess, so the confessor has to take it a little bit further to coax the individual to think hard about their crimes. Usually to the point of the penance afterwards being more merciful than the coaxing itself.
Witch Finders fulfill much the same function, except are far more pro-active in "finding" sinners but are not necessarily required to be ordained priests, and many of whom are actually Inquisitors-in-training. Results can vary in their effectiveness in finding heretics though, since they usually take a religious approach to determining the guilty rather than an investigative approach like normal "sane" people. Some examples of this crazy manner of determining guilt is to lock a suspect in an airlock and evacuate the air for an hour, Or to bury a suspect to his neck in sand and sew their mouth shut and leave them for a week... if they survive then they are deemed a witch and must be incinerated. While this is logically true, since if they survive they MUST be supernatural, it doesn't seem very hopeful for the innocent now does it? At least the Inquisition-proper occasionally gives you some intelligent form of investigation, even if you still die for being innocent.
- Arch-Confessor Kyrinov, an Arch-Confessor who uses overt loud-mouthed preaching to conceal the fact that he's a cunning manipulator, often subverting heresies from within.
- Uriah Jacobus, a belligerent old missionary who combines won't stop spreading the word of the Emperor to the darkest parts of the galaxy even though a sane person probably would've retired decades ago.
- Cardinal Armandus Helfire, a bear of a man, Helfire can often be found leading Wars of Faith against Chaos forces near the Eye of Terror. Despite his station, he can often be found living and fighting amongst the soldiers he leads.
- Witch Finder Tantalid