I'm a  big fan of story lines involving a person or a group of people finding their noble mission was actually ill intent but an evil group of people from the background. You know, conspiracy stories. (Good examples: Full Metal Alchemist, Harry Potter with the Ministry of Magic thing, etc.)

Maybe it could be a mix of both. Group of people on an expedition finding out they're actually there for some evil pirate-like (or may the pirates are controlling them. Think Pirates of the Caribbean 3. If you've seen it recently, you'll know the betrayals and alliances get real confusing throughout the whole movie. The pirates are good? The East Indian Trading company is evil pirate-supporting/killing... god, I can't think about it right now...)

Maybe they've been sent to eliminate some native race. (That's your Atlantis for you.) Or some magic artifact that could fall into the wrong hands is the target.

Kay, it's late and I'm mostly rambling now, but what I'm saying is maybe we could combine the ideas. We either could or don't have to be pirates, but maybe pirates could be worked into it.

God, I need to go to sleep...

I vote for a different thing: start another Fiasco AND this one without pirates and ships. Everybody wins! (specially me, since I'll be in both of them)