Note: This article discusses material that was once considered canon but whose canonicity is now questionable.
The Illuminati is an Imperium-spanning secret society whose hidden objectives are declared to be in support of humanity and the Emperor, and against the Forces of Chaos. The Illuminati is mainly composed of humans who have not only survived possession by a Warp entity, but also managed to do the seemingly impossible, i.e., cast out the daemon from their own bodies. The experience of sharing a mind with a daemon has completely changed their outlook on the universe, and given them a unique understanding of Chaos and Warp entities in general. In the process of freeing themselves from daemonic possession, they have also mastered the Chaos within themselves, which is the root of all human corruption by the Ruinous Powers. Apparently, they are thus unique in being able to exist in the Warp as comfortably as in realspace, without any special protections or psychic wards, and with no ill effects whatsoever since they are now immune to the effects of Chaos. There are Illuminati among the most secretive elements of the Imperium, including the Ordo Malleus of the Inquisition. In fact they seem to be actively trying to recruit Inquisitors who may be sympathetic to their plans, and/or are judged to be suitable candidates for "Illumination". Illumination is achieved by candidates who are willingly (or perhaps, unwillingly) subjected to daemonic possession, and who subsequently prove able to cast the daemon out.
The purpose of the Illuminati is to discover, groom, hide, and protect the so-called Sensei. These individuals are the biological sons of the Emperor of Mankind who were conceived before the establishment of the Imperium, and are said to be immortal as well as sterile. They possibly number in the thousands, and they are normally unaware of their heritage; also, they are psychic Blanks who possess no presence in the Warp and cannot be effected by psychic powers. As such, they are invisible even to the Emperor Himself in His current ascended state. The Sons of the Emperor that the Illuminati inform of their true nature become the Sensei "Knights of the Long Watch".
The plan of the Illuminati is to collect as many of the Sensei as they can, and then sacrifice them at the proper time, possibly as late as the exact moment the Emperor's power finally wanes and His physical body undergoes its final death, which could be millenia hence. The sacrifice of the Sensei is supposed to give birth to the Star Child. This is an entity that would be the Emperor Reborn, as it fuses the essence of the Sensei (carriers of the Emperor's physical DNA), with the remnants of the Emperor's soul -- which was cast into the Warp during the climactic events of the Horus Heresy. It is postulated that the Emperor's soul in the Warp acts as a "shining path", visible to certain individuals of psychic ability. Accordingly, it is a benign element in the otherwise hostile Warp environment, as it consists of the essence of the Emperor's humanity, compassion, and moral nobility. The force of the Emperor's rebirth (as the "Numen", the shining-path-incarnate), would then destroy the Chaos Gods, and restore the Warp to its original, psychically-unpolluted and Chaos-free state.
The impetus behind the whole enterprise of the Illuminati is the slow but seemingly inexorable advance of Chaos in the universe, and the idea that the Emperor's power, including the intensity of the Astronomican, is slowly waning as the Emperor's life gradually fails. The continuing maintenance of the Golden Throne itself is now considered beyond the capabilities of the Adeptus Mechanicus in the late 41st Millennium and there are even questions about the integrity of the Emperor's mind.
The Eldar Connection
The Illuminati are secretly allied with, and assisted in their plan by, elements of the higher echelons of the Craftworld Eldar's hierarchy, specifically certain Farseers and Harlequins. Thanks to this allegiance and their immunity to Chaos, at least some of the Illuminati are among the very few beings in the universe allowed to enter -- albeit under escort and possibly blindfolded -- the fabled Black Library, the Eldar race's ancient repository for their knowledge of Chaos, which resides deep inside the Webway. Through this access the Illuminati gained even greater understanding -- they have learned of the Fall of the Eldar and the true origins of the Emperor as the epitome of mankind's ancient shamans.
The Eldar, whose own power and numbers are greatly diminished, and who have their own reasons for fearing the continuing encroachment of Chaos, are trying to assert some sort of behind-the-scenes political power over the human-ruled galaxy by positioning themselves as counselors and allies of the Illuminati. It is uncertain how forthright the Eldar are on this issue, and whether or not they are manipulating the Illuminati to their own ends. Indeed, it is not entirely clear whether the "Sons of the Emperor" actually exist, or whether they are an Eldar or -- according to one plotline -- a Chaos ploy to mislead the Illuminati and therefore the Imperium. It is also hinted that the Eldar may have other reasons for involving themselves with the Illuminati, besides enhancing mere political influence over the Imperium. Still, there have been instances of persons proclaiming to be the "immortal Son of the Emperor". Obviously such persons are immediately persecuted by the Imperium as mutant Heretics, hence the need on the part of the Illuminati to protect such possible candidates for Sensei status, and to actively disrupt the Inquisition in its actions against such Heretics.
The Ordo Hydra
According to the Illuminati's plans, the timing of the birth of the Star Child is of the greatest importance. In order to have the best chance of success, and achieve maximum effect, it must happen at the end of a "long watch", i.e. when, all, or at least the majority of, the Sons of the Emperor have been found and "groomed" for their purpose. Therefore, the Emperor Himself must remain ignorant of the existence of the Illuminati and their plans. Otherwise, He may be tempted to end his constant, terrible torment on the Golden Throne by ceding his Mission to the Sensei, thus relinquishing His vigilance over the Imperium prematurely, with catastrophic results. On the other hand, the latest the attempted rebirth must happen is as the Emperor finally expires -- as even a solar second later may be too late.
This uncertain and possibly very long-term timeline, coupled with fanatical hate of Chaos on the part of some of the Illuminati, has apparently given rise to an extremist offshoot of the organisation -- a secret society within a secret society --the so-called Ordo Hydra. The Ordo Hydra believes its own plans against Chaos -- a radical scheme of using a "controlled" Warp "mind-virus" -- can succeed a lot quicker than the timeline of the "long watch". At most, they think it would take standard centuries, whereas the "watch" could take Terran millennia. The "mainstream" Illuminati are trying to stop the Ordo Hydra as the implications of its plans could be detrimental and/or catastrophic to humanity and the Imperium, whether these plans are successful or not.
The Illuminati were first introduced in the late 1980s' Realm of Chaos: Slaves to Darkness sourcebook. It is uncertain where they stand in the present chronology of the Warhammer 40,000 universe, or even if they are still an official part of it at all. As the Illuminati plot thread was linked to the Starchild/Sensei storyline, publisher Games Workshop may have abandoned the Illuminati storyline as the Starchild/Sensei plot was written off as yet another manipulation of the Chaos God Tzeentch (in the 3rd Edition rulebook), although other, more recent literature seems to imply that it is still a viable canon plotline, such as seen in Xenology. Most of the above lore is contained in the Inquisition War trilogy omnibus edition by Ian Watson, published in 2009 (see below).
- The Inquisition War (Omnibus Novel) by Ian Watson (contains the novels Draco, itself previously released as Inquisitor, Harlequin and Chaos Child, as well as two interconnecting short stories)