J-Dawg said:
I really like the idea that---as evil and unlikeble as a ruler as the Emperor is---the PC's pretty much have to end up protecting and supporting him because the alternative is much worse.
Do not discount the possibility that the PCs will decide to destroy the emperor anyway (assuming they can), then take their chances with the fiends. As a player, I've frequently been an advocate of "simplifying the equation" by killing those evil beings who try to manipulate the party.
J-Dawg said:
Still trying to imagine other potential missions the PC's could be sent on.
It might help if you tell us what kind of game you like to run, or what kind of game your players want to play. Site-based adventures? (a.k.a. "dungeons") Event-based adventures? Free-form personality motivated adventures? (in which you make up detailed NPCs and their goals, then insert the PCs... mayhem ensues)
In general, when the PCs start out, they could be working for the Inquisition on various little tasks appropriate to their level. As they advance in power and prestige, they move in higher and higher circles, until they start working for the emperor himself. You can make the emperor as sympathetic or unsympathetic as you want -- maybe the PCs genuinely want to help him (at first, before they know the truth); or maybe they are simply cowed into line by compulsion magic, blackmail, or the like.
This would lend itself to a lot of site-based adventures, or a traditional object-focused quest (find the McGuffin).
At some point the PCs are approached by agents of the fiends who want them to turn on the emperor. And, as noted above, maybe the PCs do this. Then you can get them involved in multiple layers of backstabbing and diplomacy, with the PCs trying to play one side off against another while the fiends do the same to the PCs.
This would lend itself to personality motivated adventures with a lot of free-form roleplaying. You as the DM would [-]steal[/-] adopt the players' best ideas about what is going on and make them true.
At some other point the PCs are approached by some kind of good-aligned organization that wants the PCs to refuse to work with either the emperor or the fiends. There's no choosing the lesser of two evils for this group; just utter refusal to let the evil ends justify the mean. Maybe this group has found another way out of the mess (unseal the good-aligned planes so an army of righteous angels can cleanse the cosmos?), or maybe this group is just a bunch of Lawful Stupid do-gooders.
This would lend itself to event-based adventures in which the good-aligned organization pursues its timeline, while the PCs either assist them or work at crosspurposes.
If you want nitty gritty advice on adventure design -- choosing EL appropriate monsters, inventing interesting locations, placing enticing treasure -- that's a whole different story, of course.