User blog comment:Solomus-BlackWing/A Legacy (Pt. 2)/@comment-2253300-20140415231910

Here's my idea in a nutshell. The three Inquisitors defected for one of two reasons. The first is that they did not believe that they could do any more good within the Inquisition. While Inquisitors have a great deal of freedom and power there are still lines they aren't allowed to cross. These three may have gone rogue in order to pursue more radical avenues towards mankind's survival than even the Inquisition would allow.

The second reason is a bit more basic. Inquisitors are given a great deal of power, but that power is not truly theirs. It is given to them so that they may serve the Imperium and the Emperor. Maybe these three were simply tired of being trapped in eternal servitude to the Imperium, which did little to reward and appreciate their efforts. Maybe they felt it was about time that they called the shots.

Thus they left, using resources and contacts that they were building prior to going rogue in order to make an organization to prusue their agendas. If we use the first reason this organization would try to gain power, and use methods beyond what is acceptable to the Imperium in order to preserve humanity. They might even want to replace the Imperium outright. If it's the second reason the organization would be devoted towards gaining power, and serving the individual interests of their masters.