This started on the general forums with a topic about Fixing the Black Sepulchre where it was mentioned that the issue lies not just with the Black Sepulchre, but the Apostasy Gambit as a whole. So I'm pretty sure we all know that The Apostasy Gambit has problems. But there are many arguments about how it has potential, and though it does seem like a daunting task to re-work it, I would like to contribute as much as I can, even if it is unappreciated by anyone but my players.
I'd appreciate only constructive posts(if any) to help the GMs that want to make this Trilogy worthwhile. That being said....
SPOILERS AHEAD!
Here's my proposed scenario arc to the trilogy. There are minor changes, with a few things added/removed based on their relevance.
Black Sepulchre
Assault on Thrungg's Mansion
Investigation of the Haemetite Estate
Enter the Titan
Fight the Dei-Phage with the Titan
Warp-induced vision from the Dei-Phage's "death" - clue leading to Arch-Cardinal
Church of the Damned
Investigate the Arch-Cardinal for signs of heresy
Find that the Arch-Cardinal has been in contact with the underhive criminal: Venomskin
Investigate Venomskin; Learn that Ignato has escaped to Stonegarden
Attacked during journey to Stonegarden
Witness the resurrection of Saint Drusus
Chaos Commandment
Sector is plunged into Chaos by Drusus's resurrection/Dei-Phage possession
Assault on bunker outside Hive Tertiam, encountering "the Oracle"
Find that the Oracle's local noble house is harbouring a blasphemous Prophet of St. Drusus, Molokor Kambyses
Investigate Molokor Kambyses in Hive Tertiam, extract him into the Inquisition's custody - alive or dead
Kambyses' daemon-possessed warp-ghost kills patron Inquisitor, survival horror commence Dead Space style
Release Kambyses' spirit from possession, learn the location of St. Drusus to be on Grangold
Travel to secret hiding place, find that St. Drusus is inside a warp-realm
Enter the warp-realm to final showdown with St. Drusus/Dei-Phage
Anything missing from these bullet points is most likely intentional, I removed some parts. Otherwise, I plan to expand on most of every point above.