Undead Plague

From the introduction:

This adventure can be can be easily customized to a party of any size or level, or run as a level 3 adventure for 5 players. It can work as a small side adventure in an existing campaign, as a standalone one-shot, or the start of a new adventure. Use the links to the tools in their relevant section to customize the adventure to your party.

The players learn that rat catchers are going missing under the city and a plague is spreading in their absence.
Most of the populace is sick, a DC 10 Medicine check can identify it as a contagious plague spread by rats.
If the PCs go searching for rats, they'll find that most of them seem to be coming from under the city.