The Following Sea by Marsha Canham

This time the story focuses on Gabriel Dante, taking up where The Iron Rose left off, as he sails away from battle with horrendous wounds and half a crew on board a captured ship. On his way home to the safety of Pigeon Cay, Dante crosses paths with a strange ship sailing in circles, showing no signs of life on her deserted decks. It is a plague ship, flying a yellow flag, warning all sailors to stay away.
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On board the Eliza Jane, Evangeline Chandler is the only survivor of the fever that wiped out the entire crew. Eva, weak from thirst and hunger, wakens to find death screaming across the sea, as a full broadside from Dante’s ship explodes around her.