Noumenon
First Post
My thinking was that they would begin swarming through the area where the PCs once stood, attempting to ram anything hidden there.
That's one obvious way to find an invisible creature that the rules don't cover at all -- all those rules about "attack into two adjacent squares" seem to imply just moving through them wouldn't work. I think it should. It doesn't even explain anywhere what happens when you move into an invisible ogre's space.
It seems that your PC's are flying low under the radar, just as Frodo did on his epic quest to destroy the One Ring
If you have the creativity and time, this sounds like a really suspenseful and cool way to start a campaign. Deep in the enemy's stronghold the whole time. I was gonna suggest you copy the plot of Douglas Hill's Master of Fiends, but I got sidetracked reading an eighteen-part takedown of it on LiveJournal and don't have time to summarize any more. Basically have them find some kind of slave race, have some fights to win their trust, then they give you the weapons you need to actually face the huge mass of storm spirits that totally outnumber you. It just sounds a lot cooler to me than the option you're thinking of which is "I'm gonna let them get in even further over their heads and sink." The illusion of being totally beyond their depth is what you want to provide, it'll make everything so much more suspenseful than a typical campaign.