Well, this is only the second one I've written out, and it's very much a WIP.
"The group was stolen, and kidnapped by the Amaranthine Syndicate, and is currently being used by said peoples. They were picked up by the Syndicate due to the general ideal of why Acolytes are picked up by the Inquisition; they are above and beyond all others.
They get used to do some horrible crimes (planning on making them start riots, kill large groups of innocents, cause problems essientially) and get to be generally used for other purposes as well. They are getting used by the Syndicate in order to expand trading, due to a massive uproar for needing materials that the Syndicate 'happens' to have a swack of.
They eventually get stumbled upon by the Inquisition and drafted, due to 'coming across' a group of Acolytes. The said group of Acolytes were sent to find them, due to the said crimes that have been happening, on a suspicion of cult work, and they are told to bring them in. While the Acolytes find them, they are doing a mission for the Syndicate of high-importance, and they'll fail it (due to being pulled in by the =][=), they piss off the Syndicate, badly.
(If they kill the Acolytes, an Interrogator ment to meet them comes in with his bodyguards. If they allow theirselves taken in, they get onto a transport, sent out for a brutal interrogation and the Inquisition find out the truth.)
Afterwards, they find out that it turns out they were kidnapped, and nothing they were told by the Syndicate is true (Told by the "Black-Room Man" that they were removed from all of their organisations, like Arbitrators from the Adeptus Arbites, PDF Trooper from PDF, etc.) and that they were simply duped.
They get sent to track down the "Black-Room Man", and through a series of trails; they end up killing him, to simply find out, another small twist, he was next to nothing, only a small part and front of the Syndicate. They have to go more in depth and get deeper down into the Syndicate through various missions and such."
That's my general idea. Feel free to rip apart, I know I haven't thought of everything, and need some help to make this more concreate and for me to have a better idea.