If it were me, I'd look at this as a last chapter and work the story back from there. You need to establish the story of how the Phoenix was lost. A bit of background on the present pirate problem, the story of the Howler's lost launch and the poor female prisoners might do. This could be developed to emphasize the growing and more general pirate problem, you might find an arch villain useful as well. Do these slavers only let the female prisoners live? Then work in the arrogance from both sides the pirates becoming bolder as their power grows and the Military relying on poor intel and refusing to take the problem seriously; sending good ships out to be slaughtered piecemeal.
You also need to establish a fantasy rule/reason that requires/allows/causes the ghost ship to intervene and prevent disaster. This should be hinted at in the beginning chapter that establishes the myth of the Phoenix and then threaded in throughout the rest of the story.
It would be a project... three chapters minimum maybe as much as five.
Your choice Rhabbi