Sometimes players zag when you expected them to zig. It happens to all of us. Often it’s easy to just adapt your current adventure to the changing situation. However, sometimes it isn’t…
It helps to remember that RPGs got their inspiration from pulp fiction stories, the sort of tales where coincidences keep popping up like first graders on Christmas morning. So your players decide to go gallivanting off on some diversion, big deal. Who says the bad guys aren’t already there?
So your players go off to the City of Townsville instead of the Town of Citysville. Mojo Jojo is supposed to have something nefarious planned in Townsville, doesn’t mean he can’t have something planned in Citysville. We’re not exactly talking about reality. Heck, we’re not even talking about good writing. If you want things to just happen because you damn well feel like it, let them happen.
Besides, in real life events don’t have to make sense. When running an RPG you don’t have to make a publisher or editor happy, as long as your players get into it.