Shades of Lovecraft's "The Rats in the Walls!" Clearly, the rats are being driven up from some lower, unknown benighted region, whether an Underdark-like realm or an aberrant wisp of some terrible demiplane. The Presence inhabiting the space plans to become a god, and has been entering the innkeeper's dreams, driving the keeper to prepare the way. The Presence needs acolytes to build its religion, so the keeper is tasked with finding "worthy applicants" (though the keeper may not realize it). The rats - and the worse things chasing them - are but the first of several tests applicants must "pass." Using the keeper as a puppet, the Presence will deliver additional rumours and intriguing info to the PCs that drive them to other adventures that further the apotheosis - retrieving or destroying certain artifacts/relics, eliminating rivals of and threats to the Presence, acquiring exotic materials, etc. Many levels later, when the Presence is ready for ascension and its priesthood has grown (the PCs weren't the only adventurers groomed this way), and the PCs have adopted the keeper as a trusted friend, will their "final test" be revealed - returning again to the cellar and a new more horrifying infestation, revealing the Presence, its burgeoning priesthood, and the PC complicity in the swell of power. And a choice: serve alive or dead!
Or maybe that's less lampshading and more like overthrusting.
Okay, they aren't rodents, they're a gang called "The Rats," regulars at the inn. The keeper got drunk one night, gambled with them, bet the inn, and lost. The keep signed over the deed that night, but after sobering up doesn't want to honor the bet. The Rats have moved into the cellar and refuse to leave or allow the keeper to access the stores. The issue is pending before the magistrate, but the Rats have a pretty solid case. The keeper's decided that some passing adventurers happening to eliminate the "rats" is the way to go. The difficulty can be modified by whether the Rats are common folk, wererats, a mix of were-types, dopplegangers, whatevers, or connected to a larger organized crime ring, etc. It could become the basis for contacts for your rogues, a nemesis for the party, etc. Or the situation could be resolved peacefully - the Rats do like gambling and showing off, so some diplomacy, gambling, cajoling, etc. could go a long way. Or the PCs could side with the Rats, in which case the keeper could be a surprising threat, whether a mage, were-something, super-mummy, etc.