SPOILERS

I'm running The Black Sepulchre and it's been a blast so far, but I have an issue wrapping my head around what exactly the Black Sepulchre is. An odd machine, built long ago, enshrined in an Imperial Cathedral….and it decodes a video when planets are properly aligned? That's pretty ridiculous. Am I missing something? Can anyone make this make sense? I'll probably skip that end scene and just give them the vid-pict, but they're gonna want to know what was under the sheet at some time.

From my reading of the Black Sepulchre, the thing itself is sequel bait, plain and simple.  It is simply an object to connect the first adventure to the next.

If you wish to describe it, however, think of it like a shrine-like holodeck from Star Trek.  It was made for one purpose and one purpose only- to decode an overly elaborate Inquisition code using arcane and Cthulhu-esque sciences to reveal a secret so hideous it could bring the Calixis Sector to ruin.  If you want a better explanation, say the machine draws on the powers of the local warp swirls of Baraspine, waiting for that right moment to spill its secret.  If you wish, have others hunting the secret- make it a race to keep whatever is on the holo-tape a secret.  If the acolytes fail, the secret (whatever you choose it to be) will be leaked out and the Calixis Sector may turn to Chaos.

 you could always use my solution, which was a warp-induced vision showing essentially the same thing, but less "it has to happen this way with the stars aligned blah blah"

Correcting the Apostasy Gambit