Hmm... agents stuck in city, they blame VILE, VILE comes walking through the area blaming ACME, then they team up to battle an evil clown... oh, wait... some guy I've never heard of wrote that already.
We could maybe have it be non-canon and invoke some reasonable amount of Sci-Fi (nothing too incredibly outlandish)... just a random 'have some fun with it and see what comes out' kind of story. Could be vampires, ghosts, maybe a Freddy Kruger-type guy, alien invasion, super-plague, The Blob, secret society... pick your horror/mystery trope and maybe toss some comedy in there for good measure... maybe a crashed UFO or friendly aliens to taste, let cook for a few pages or until suitably done... season with anything you can think of to make it chooch better.
(Yeah, I'm a geek)