I have been running my campaign for a few sessions and the players have decided to go into a city that unbeknownst to them has a wererat problem. The players are 3rd level and I have been generous enough to give them two +1 weapons. Any tipis on running this adventure, especially since I am kind of new to city based adventures.
There should be a rash of thefts and back alley murders plaguing the city. Some of these may be simply "random acts of evil," but some of them should have a purpose. Why are the wererats growing their numbers at this time and what are their aims?
Consider the environmental impact that wererats have. If the wererats are carrying disease, maybe there's a plague epidemic or a quarantined district. Maybe the sewers swarm with rats/dire rats and the Ratcatcher's Guild has more work than it knows what to do with. Maybe an attempt to poison the sewers has tainted the water supply in the slums?
Consider their points of egress/ingress in their underworld lair. Cellars, catacombs, vaults, aqueducts... discovering and sealing these points of egress/ingress can help the PCs define the field of battle.
I'm a sly, avaricious lycanthrope who can only be hurt by magical or silver weapons. Heh! I know! Let's gank whoever makes/sells those weapons in the city. Better yet, let's incriminate someone else for ganking them. Or even better still, let's blackmail them or leverage politicians to require bladed weapons to be peace-bonded or silver/magic weapons to be registered.
They operate like a thieves' guild that is aggressively (and selectively) recruiting. Other criminal organizations may feel threatened and conduct their own investigation into the wererat threat. Maybe rogue PCs can go undercover...if he/she can first survive "The Rat King's Trials".
Lastly, they're Neutral Evil and the MM says that wererats who are accidentally cursed or break free of the "guild" are hunted down. Sounds like a great opportunity for a selfish wererat exile NPC who could become their guide through the sewers below...but whether or not they trust him is another matter.