The present leader of the Brotherhood is known as the Cardinal - Cardinal Nathaniel Durand XVII (renamed in honor of the original Cardinal Durand). Although the Brotherhood has its roots in Christianity, at the time of its formation, it embraced "all religions", and has become a religion all its own. The original Cardinal has been nearly deified, and is often prayed to. Common people even pray to the current reigning Cardinal. While there is just one head of the Brotherhood, there are other Cardinals (also known as Sheriffs) who preside over the major Cathedrals built on each planet in the human worlds.

The Brotherhood was formed as a result of the efforts of a single man who would go on to become the first Cardinal, and who is the first person known to be able to practice the Art - which he claimed was a gift from God, that all people could learn to use, in order to fight the Darkness. This first Cardinal came from Bauhaus, and Bauhaus was accordingly very dedicated to helping in the creation of the Brotherhood's structure. The Edicts of Thoth - declarations by an influential Mystic serving under Cardinal Durand - were issued, prohibiting a number of technologies deemed too easily corrupted by the Dark Symmetry, or perhaps even inherently evil. Among these were cybernetic enhancements of the human body, genetic engineering, the manufacture and use of "thinking machines" (computers), and various restrictions on technologies deemed sufficiently complex to attract the meddling of the Dark Symmetry.

The Brotherhood was instrumental in a number of counter-offensives to drive back the Dark Legion, and for a time was very influential in human societies across all of the terraformed planets. However, when the Dark Legion seemed to be relenting, people grew complacent. Whole generations lived and died without ever really experiencing the horrors of the Dark Legion - at least, not in any form they could recognize as such. The purpose of the Brotherhood's existence grew confused at times - as it is an organization with very religious trappings, yet it is not truly a religion ... unless the Art itself is the Brotherhood's religion.

In time, the corporations became a little less convinced of the necessity of the Brotherhood and its restrictions imposed upon technology. This was best illustrated by the emergence of the new, fifth megacorporation, Cybertronic, which basically spat in the face of the Cardinal and set up its own Orwellian society on secluded asteroid bases on the far reaches of human-occupied space in the solar system. Mishima, long antagonistic to the Brotherhood, was emboldened by this, and all but banned Brotherhood activities on Mercury. The megacorporations have been pushing the line of the Edicts of Thoth, and sometimes dealing with Cybertronic for use of its innovations. Bauhaus still at least claims allegiance to the Brotherhood, while Capitol can be described as "friendly". Imperial claims, too, to be loyal to the Brotherhood, but in practice it mostly just uses this as an excuse to justify its attacks on other megacorporate interests, claiming Cybertronic of Dark Legion influences on whatever it decides to raid and assimilate.

In recent decades, it has become evident that the Dark Legion is very active, as Citadels have begun to pop up on the human worlds with greater frequency, and it has become more bold in its use of cultists in human cities to spawn campaigns of terror and to unleash virulent diseases in population centers. Despite all of this, the average member of the populace seems downright determined to believe in more humanistic explanations for all of this supernatural activity, and even those who acknowledge the existence of the Dark Legion seem to think of it as perhaps a new, sixth megacorporation entering on the scene.

In its desperation, the Brotherhood has taken to fighting darkness with darkness, taking a notion of "the end justifies the means" in its treatment of ordinary people while it seeks to root out Heretics. If a powerful Heretic were to take shelter in a shopping center filled with civilians, the Brotherhood could well deem it an acceptable "if sad" loss, to bomb the center and accept civilian casualties, if it would guarantee that the Heretic would be killed in the process, and if it could be justified that his survival could mean even more deaths and corruption. (Of course, such a thing would be set up to appear to be a terrorist action on the part of the Heretic in question. The public isn't that accepting of Brotherhood excesses, after all.)