The traditional storylines are:
* Dealing with a thieves' guild that has done something where the PCs need to fight their way in and recover/stop,
* Fighting off an invasion (I like aberration invasions for a good Cthulhu feel - but undead, demons, cultists, fey, orcs, giants, flumphs, etc.. could all be interesting invaders),
* Political intrigue where powerful members of the aristocracy use the PCs as a pawn in a diplomatic battle (perhaps framing them for an assassination), and
* Exploring a dungeon beneath the city.
If you have established areas in your world, I suggest writing your own urban adventure rather than converting a preexisting one. It allows you to pull in those essential elements that make the world your own. Those elements are often more visible in an urban setting with a sense or order rather than in the chaotic wilds surrounding civilization.