I personally couldn't bear it either, and I'm not too sure what it was about either (though I forced myself to watch it twice), but I'll try my best.
In a nutshell, the whole movie was some stupid thing about these thugs looking for some "treasure". They don't know what the treasure is, they just know it's a treasure. Also, there's this fat museum owner who wants the treature, too, I think. So he somehow has a riddle map thing that one of the two pirates ladies had (Forgot whether it was Mary Reed or Anne Bonnie. In fact, I don't even know if I spelled their names right), and he has a treasure hunt involving the map so he can lay claim to the "treasure" when someone finds it. Those are the main "antagonists", so to speak, of the whole movie. It's pretty apparent from the start, and a few red herrings were thrown in there that really didn't even make a difference. Somehow, the movie managed to stretch for a whole 1 hour and who knows how long it's been (everyone's just about asleep by now anyway), the thugs kidnap Ran and Sonoko (Ran somehow lost her karate powers from this point forward), force them along in a cave in an island, force them to unlock doors and test rooms for poison, and then finally they reach the treasure. And guess what? The treasure isn't a real treasure, it's a ship! Gasp! Wow, I didn't see that coming... So yeah, now the thugs are angry but then it's Conan to the rescue before Ran and Sonoko become shark bait. Then they run into the fat museum owner who somehow managed to follow them in the cave. Conan talks for a while, but no one can really understand what he's saying because half the stuff he talks about the audiance missed while they dozed off. After that, the cave starts flooding for no apparent whatsoever (what a coincidence), and Conan kicks a metal chain into the ceiling to ignite some gunpowdered rock I think. Everyone uses the oxygen tank thing, but Conan doesn't have one, so as the ship (with Ran, Conan, Sonoko, fat museum man, and the thugs in tow) rises out of the cave and into the open ocean, Ran gives Conan her air tank (this scene lasts 3 seconds, so be sure not to blink or else you'll miss it). After that, the movie is over, the ship collapses and sinks to the bottom of the ocean (just because they had no better way to end it), and it's the end.
I know I didn't explain very well, but that's about all I got from the movie.
If you don't get it, who cares? It's not worth understanding.