Wednesday Boy
The Nerd WhoFell to Earth
2) Do I let them do what they've planned on doing, and let them deal with the consequences of not finding the other layers? (oh that will would be evil and fun to deal with in it's own right! and my prep-work is then easily recycled in to further plot and story with minimal effort)
I like Option #2. It lets the players choose their path with no railroading (although as a player I think a railroading is not necessarily a bad thing) and as Spiral Cat mentioned can serve as a major clue to getting them into your major plot.
As a player I love intrigue plots and it would be very interesting to come across the fallout of some evil plan that happened because the party didn't pick up on clues. I'd find it very rewarding if our party could CSI it up to figure out what happened and then do some deductive reasoning to connect it to what we'd already over looked in previous sessions. And it would hopefully give you the chance to get your plans back on track!