Ecclesiarchy

"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."

-C.S. Lewis

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 Imperium spares no expense on it's houses of worship, unfortunately we can't say the same about civilian accommodations...

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 science and reason now". 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 daemons when lines from it were spoken to them. Suitably embarrassed, the Emperor politely informed Lorgar to stop worshiping him the bullshit. 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. Somewhat unsurprisingly, especially when he forced Lorgar to bow to one of those smurfs 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. The Emperor was not particularly empathetic The Emprah, beloved by All, was saddened.

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 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, starting the Age of Apostasy. After that, the Ecclesiarchy started becoming what every powerful group in the Imperium does: more interested in its own power than the people they're supposed to be ministering to, and public funds and taxes ended up funneling their way into the church, and 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.

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" to rename themselves the "Brides of the Emperor" and become his bodyguards, they were also give 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.

Thorian Reformation

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!

Temple Tendency

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."

Organisation

At the top of the organisation is the Ecclesiarch himself, who is essentially the Space Pope and the equal-first 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.

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 fulfil 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.