A simple one would be to purify some kind of artifact. Take the most religious member of your party (let's just assume it's a cleric) and design a quest around the cleric purifying something like a holy symbol belonging to a high priest of old. Said holy symbol has been tainted by foul dark magic. Different tasks could resemble different feats or points in time for the cleric's deity.
How does the rest of the party get involved? Let's say that the holy symbol was tainted by cultists of a god that rivals another party members. They might need to visit their church or talk to an inquisitor and figure out proper means to combat these cultists. Several deities have allies and their allies have similar enemies so that could tie other party members in. Check out Inner Sea Gods for tons of information.
If it was for a cleric of Iomedae you could even make the holy symbol one of Aroden and that ties in a whole bunch of gods. To the Pharasmite it could provide answers to the deities death, to the Caydenite it represents another mortal turned god. There is a lot to work with if you use Aroden as he is a dead deity with ties to lots of other deities.
Well, I am not sure I totally understand but will try to help. First consider the diff between acts of faith and lives of faith.
Silver medal for faith: david vs goliath. A 14 year old goat herder takes on and kills a dude the size of shaquiel oneil raised to fight since birth with a single rock. Balls!
Gold medal: abraham. Kill your son, says God. Sure thing, says Abe.
These are acts of faith. Lives of faith: joan of arc, francis of asissi, mother theresa. Folks who put the ideals of their god above their own. It takes special players to do this well.
Each arc will need at least one act of faith and each chapter should have a theme of service to the God. Different gods being served differently of course.
Here's some ideas I like:
Dark(ish) - A vampire lord seeking godhood is slain by the rival god of X, lifting the curse of vampirism from a cadre of warriors, paladins and clerics. The god of X demands their fealty in exchange for returning their powers. The PCs awake in coffins in tattered clothes, with ancient gear of bronze and must fight their way out of the center of a dungeon to prepare the way and herald the coming of their god's avatar who plans to walk among mortals in order to punish/remind them of whats whats.
Bright - each PC is infused with the spirit of an angel and must use their new sacred gifts to route an evil serpent cult, claiming their temples for their own. This would include not only combat but resource management and church building (raising funds, defenses, temple guards and conciliating good will among the people).
"That country needs the light of JEEEESUS-AH, bring it to them via blood and steel my holy warrior" seems to have been a popular one throughout history.
Important question: Is this about the faiths of the PCs (do they have the same faith?) or is it centered around NPCs?
Okay. One idea might be:
An elderly member of one of the PC's faiths has long been a fervent believer, but as death closes in ze begins to question hir own convictions, having become bitter over the years. The PC's (especially the one who shares hir faith) has to somehow convince hir that faith is worthwhile, or maybe they themselves get influenced by the old person.
A beloved member of the church is dying, of natural causes, and he has accepted his death with grace and humility. But vile daemons and other soul stealing outsiders are gathering to besiege the temple where he lies in hopes of stealing his soul away to devour or sell to enemies of the church.
A fiend has kidnapped one of the gods favored servants, a direct assault would bring a catastrophic war between heaven and the lower planes. You must rescue him/her.
A schism has recently erupted in the faithful, some suspect it to be the work of outside influences. You must uncover the source of this schism (a rakshasa) and reconcile the differences between the bickering groups.
"But who's to say if it's right or not?"
"Who's to say if any of the gods are right? If you start down that path, you end up worshiping no one, or Ao, simply because he created you."
This is a quote from a very good NWN2 fanfic that is deals a lot about the relationship between a deity and their followers. Not exactly what you're looking for I don't think, but it would definitely help generate ideas.
A simple thing I do as a gm is to actually have the player communicate with the object of their faith. For example, when they're praying for spells in the morning, I will let them know if their deity is pleased with their previous day, or maybe drop hints as to what spells might be useful for the upcoming day. Little stuff like that. Again, this is more personal for an individual pc, and so now quite what you seem to be looking for I think, but it would definitely inspire some good rp.