Ordo Malleus and that unusual potrusion!

The first Inquisition was founded with the express purpose of preventing another Horus Heresy. The men and women at that time did not, nor could they forsee how far down the rabbit hole the Imperium would go, nor could they have anticipated how strong the cult Imperialis would become... The first (chronologically) mention of the Inquisition I can think of is at the end of the Flight of the Eisenstein, where, at the end, one of the characters is approached about joining an organization to investigate and eradicate future rebellions.

The whole notion of purity is a canker in the mouth of the Emperor. It is a sore on his foot. The Emperor sought no worship, and cut down those who praised him as a god. Admittedly, the whole repulsion of daemons by Keeler suggests that there's something about His name... but, even so. The Emperor was a powerful psyker. More powerful than any other. How do we know he can't reach out across the galaxy when He's needed, by the strength of his power, not by virtue of divinity?

Regardless, the Inquisition might appear to lack the moral fiber to do its duty, but remember, the Inquisition has to have a questioning approach to everything, even itself and the Emperor, or else it won't be able to root out the heresies, daemons and xeno before they conquer mankind.

The flight of the Eisenstein does not specifically mention the formation of the inquisition. It just has Malcodor mentioning that people like Garro would be of use in the future, suggesting the formation of a militant chamber. The inquisition did not form until the 32nd Millenium. The idea came from two individuals following the Emperors assension to the throne. They believed that the MEperors spirit was ruling over the Emperor and worked closely with the surviving primarchs. They also wanted to prevent those who believed in trying to ressurect the Emperor (although the faction believeing in this was eventually reabsorbed into the inquisition).

It is unclear what the Emperors motives were (or the motives of people such as Malcador the Sigillite or Chief Custodian Valdor). These might be explored in the future. However, it is hinted that the Emperor had a delibrate plan to attain god like status, although not necessarily being tied to a corpse on the golden throne.

It is also possible that the Emperor became a god by accident. He just happened to set up the right circumstances. I interpret Keeler as being the first sign that he was nearing godhood. Basically his warp presence was so powerful it was beyond being held by the Emperoros mortal body. All he needed was mortal followers to believe in himself and he could channel his self through these followers. This is much the same way chaos gods work. What wnet wrong is that he ended up tied to a broken mortal body, rather than being a god liveing in another realm or channeled through his fully functioning mortal body.

Finally, there are many ideas within the inquisition, but all ultimately serve the Emperor who might be saveing humanity from immediate destruction, but has condemned humanity to slow steady decline and eventually being wiped out. In the meantime, the majority of humanity are pawns sufferign while a tiny elte benefit from the imperium.

As they say within the Holy Ordos. Everything you have been told is a lie. The Inquisition, contrary to popular, external and internal opinion, works best as a factionalized organization full of dark secrets, deceptions and lies. We now what they do and how they do it. I just don't think we'll ever really understand why or how they came to being.

If I remember correctly wasn't it two Thorians that were the first Inquisitors? They both wanted to bring the Emperor back but they chose two different paths. One scoured the universe for secrets while the other tried to use the power of the warp. Eventually they clashed and the one who was using the warp was defeated. She disappeared somewhere in the region of the Eye or frankly into the Eye itself while the other I have no idea. I might as well start a thread on the formation of the Inquisition.

Edit: Promeus and Moriana are the names of the resurrectionists.