Pay a visit to one of the Temples or to one of the quest givers in the Ebonheart Imperial Shrine (I started the quest line by speaking to the NPC that is right inside the door of Ald'ruhn's Temple). They will give you the quest that starts the mod.
I forgot all about this mod, should prolly try it out sometime since I love the Temple and all. Is it particularly incompatible with Darknut's GDR or Great House Dagoth? Anyone know?
I played the Great House Dagoth version of the main quest and then played the Vivec's Fate mod without any problems...although...
Spoiler
for role-playing purposes I did need to come up with an alternative way for the scene within Vivec's Palace to play out. I had gone with the "drop the moon on the palace" ending of GHD. Game mechanics-wise, there is no problem since an NPC teleports you into that cell which still exists even after you crash the moon into the palace. You can then just recall out at the end of the scene. For my own game I played out that confrontation taking place on the stairs outside the palace, so I had that crashed moon as an amusing backdrop to the meeting with the leader of the Ordinators.
But again, as far as game mechanics go, there were no problems at all.
Yeah, I thought the storylines probably didn't mesh well, which is totally cool for me. I would only attempt to play through it with a non sixth house character anyway, I just like being able to load all my mods at once.