If you game with me, stop here (this may be an adventure seed someday), or, read on if you want and write a good adventure on this 
Vampires/ghouls are plaguing the area. The characters are rounded up to investigate, track them down, and stop the creatures. A young woman energetically leads them. After a lengthy process trying to spy on the vampires, moving through the city on a secret ritualistic path, finding one riddle-like sign after another (something like Dan Brown’s puzzles in Angels & Demons), the group arrives at the lair.
Something seems wrong though, the vampires or ghouls are actually meeting to discuss something that has been killing their own kind. They are trying to decide to fight or flee. It turns out the murders recently attributed to them haven’t been caused by them, though the woman accuses them of lying.
It is then that she is recognized by the ghouls/vampires. She is an exiled member of their group. She wanted them to take power over normal people but they threw her out. She’s been gathering up some unholy army to destroy her people (actually her creatures have been doing the murders). The PCs realize they have been helping the enemy all along, killing vampires/ghouls that haven’t really been causing that much trouble. Just then her creatures break in and attack.
Ideally, the PCs should fight with the vampires against the creatures, which are indiscriminate in who they attack (except for the woman).