I like the pirate/nautical theme. I also like the non-linear idea.
How about something like this:
You start off on a mainland isthmus, where an evil bad guy has overthrown the king/queen/ruler, bringing about despair to both the land and its inhabitants for the past several years. However, legend tells of a holy/magical object that can help restore the rightful king/queen/ruler to the throne. When the evil bad guy assumed power, he dismantled this object into (x) number of pieces. Each piece is said to have been taken to a different island by the evil bad guy's fleet, where it is being guarded by some unnatural beastie.
Your job is to explore each of these islands (in a non-linear way) and recover the pieces of this holy/magical object, return them to the starting point, and help restore the rightful king/queen/ruler to the throne.
By completing the main mission on each island (in which you must defeat the unnatural beastie guardian) you recover a piece of the object. Along the way, you must find and stop off at smaller islands to replenish supplies, hire sailors and recruit captains of other vessels to form a small armada to help in completing your journey. By completing various quests for different NPCs, you bargain for the services of crew and captains as well as for supplies.
On the high seas, you encounter sea monsters, mutinies by crew members, evil bad guy ships and those who would seek the pieces of the holy/magical object for their own ill-gotten gains.
Once all the pieces of the holy/magical object have been recovered, you return them to the mainland and prepare for the final battle against the evil bad guy.
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