Mike Scaccia's metallic guitar work in Ministry's catalogue, from In Case You Didn't Feel Like Showing Up onward, is often seen as the nail that slowly secured the coffin of the band, but Scaccia and Jourgenson's work together in support of creating grindingly heavy, ugly monoliths of sound was initially that rare merge of brutal and beautiful that makes most metal I come across now seem like a defeated attempt to re-render that same formula. In fact, the only metal band from that time frame I can think of that did it better than Ministry was Godflesh* (admittedly, I don't listen to much metal though). The riffage on Psalm 69 and Filth Pig isn't a technically complicated style, but its use (and abuse) of distortion and effects pedals, particularly when combined with industrial/mechanical locked grooves, takes on an atmospheric and psychedelic quality not out of line with what was going on at the same time in the realm of shoegaze and post-rock.
Check the death's head tantra of "Scarecrow" and tell me its persistence doesn't recall Robert Hampson's textural use of feedback in Loop's discography or Main's first couple of records:
Or the way the very simple call-and-response chords of "The Fall" take on an apocalyptic grandeur when juxtaposed against twinkling pianos and a squealing noise loop synched to a jittery beat:
Unfortunately, after Filth Pig, the band did become everything fans thought they were becoming, though they had one two decent moments here and there.