The Pirates of Dark Water

The Pirates of Dark Water was released on the Sega Genesis in 1994. It us based on a cartoon of the same name that ran from February 1991 to May 1993. There was also a Super Nintendo game but it is a beat em up and different from the Genesis version.
You can select between three different characters at the beginning of a stage. Ren, Tula, or Ioz. Each have their own strengths and weaknesses, but I don't think it affects gameplay much.
From Wikipedia:
Ren, the son of the dying King Primus of Octopon, sails around the alien world of Mer on a ship called the Wraith, searching for the "Thirteen Treasures of Rule". The treasures are prophesied to save Octopon and Mer from the threat of Dark Water, an all-consuming black liquid that has taken over the seas. His loyal crew of misfits that help Ren on his journey are the ecomancer Tula, a monkey-bird Niddler, and the treasure-hungry pirate Ioz. Ren's opponent in his quest is the pirate Bloth of the warship the Maelstrom, who will stop at nothing to get the treasures and control the Dark Water himself.