I just finished reading Dan Abnett's Pariah, the first in the Bequin trilogy, which is itself the author's third trilogy about the Warhammer 40,000 universe's Inquisition. It is billed a titanic conflict between the legendary inquisitors Gregor Eisenhorn and Gideon Ravenor, both of which have tended to go rogue and take whatever measures they deemed necessary to accomplish their goals of rooting out heretics to the Imperium.
Who is in the right thus far in this conflict is far from clear. Much of the action in Pariah is setting the stage and establishing the motivations of each Inquisitor and their respective retinues, primarily by way of introducing us to one Alizabeth Bequin, a character at once familiar but strange to readers of the Eisenhorn trilogy. Writing much more would spoil a lot of the fun. Suffice it to say, if you have read the Eisenhorn and Ravenor books, you'll want to read this one, as well.
And if you haven't read Eisenhorn and Ravenor, that's actually ok, too, for the purposes of enjoying Pariah--but take my word for it, you should go read those two preceding trilogies. They are really great sci-fi renegade detective stories, tons of fun, and exist really quite apart from the Space Marines-focused galactic war stories of the rest of the universe.