The main character is Pan Gamma Vi Gen. He is the captain of the legendary black vessel.  Pan Gamma Vi Gen is lazy and clumsy -- that is him when is resting.  But once Pan decides to work, he is the best man available.  Pan says things that normal people can hardly understand.  And he doesn't say much, he only gives lots of clues. Everything starts when Captain Pan let Mia and Tuban Sanoo be aboard.  Mia is a princess of a fallen country and Tuban is the best, people say, swordsman as well as strategist.  Although Pan Gamma Vi Gen is the main character, it seems Pan, Mia and Tuban are the main characters as Mia and Tuban appear in all episodes.  Mia is looking for science to restore her county, Ontana.  Tuban is protecting Mia as the will of someone Tuban trusted.  Pan Gamma Vi Gen agreed to take Mia to where she could locate the science in exchange of her virginity. ( Don't get Pan wrong here, I believe he meant something else but at this moment, Mia's virginity is all I can guess.) 

Agreed with ghostmage.  Description above covers most of the stories so far.  Nevertheless, If you guys follows the 'Mutsu" series from KAWAHARA Masatoshi sensei there are a lot of things 'supposed' to be revealed.  The story is great, and the readers especially fans of Mutsu will often make up their own stories in their minds.  So far until vol 37, what I see is the Mutsu series of Sea Battles .  Can't wait for the melee one!  Fan just sucks at using swords!. 

Having just finished volume 42, I have to say this is my second favorite manga after One Piece.  The Description above is pretty bad at capturing the best of this story, going so far as to get the name of the main character wrong. 

Faan Ganma Bizen is one of my all time favorite characters.  He's self promoted as a lazy person who doesn't want to do much at all, in spite of being the captain of one of the most feared sailing ships on the ocean, the kagebune (Shadow ships) and wielding a nihontou (Japanese sword) a legacy of ancient times.  The story starts in a small port city where two pairs of strangers meet the mysterious captain and eventually become passengers on board his ship.  There is Mia, a young lady obsessed with the secrets of the mystical magic of "Kagaku" (Science) and her guardian Touban Sanoo who's name is almost legendary on the mainland for begin one of the greatest swordsman alive.  And then there is Prince Kazel Shei and his younger sister who are being hunted by opposition forces from their own country.  Their meeting with Faan can only be called fate as their journey takes them into the path of powerful nations and towards discovering the true nature of the mysterious Kagaku. 

While a lot of the story elements taken alone could be considered cliche, put together the make up a strong story with excellent character development (particularly of Faan) and truly entertaining and reasonably realistic relationships between them.  Faan truly comes across as charismatic and its no wonder that the other characters become drawn to him and can believe in him.  There's a lot more to be said of the overall world and story but it would mean spoilers, so just go and read it or hope a group picks this one up again. 

EDIT: Now having finished the story I have to drop the score half a point for what I feel is a weak ending to an otherwise excellent story.  It wasn't a bad ending, but it wasn't great either.  The final few volumes lacked the power and excitement of the earlier story and felt, if not rushed, generic and unrefined/unedited or average/plain.  And basically it ends with a narrative epilogue (one of the characters explains what happens in following years) that reveals too much information and destroys the energy and wonder of what the future holds for the characters.  The romantic interest angle is concluded in an original way (I'm not sure if I like it or not). 

Overall, it's still worth checking out and I hope a scanslating group picks it up seriously so others can enjoy it too.