While not technically a slave ship, you'd be forgiven if you mistook the Prophetess for one at first glance. Run by two scurrilous scalawags, Captain Molyneux and first mate Mr. Boerhaave, the Prophetess is as far from a pleasure cruise as one can get.
Pretending to run a godly ship, where "the only spirit you need is the Holy Spirit" (11.1.12), Captain Molyneux forges a trade alliance with Preacher Horrox of Bethlehem Bay, essentially turning Christian missionary work into a business investment. He's not concerned with saving souls; he's concerned with saving money. If it means that darker races work for him for next to nothing, so be it. He already has one guy, Autua, working for free.
The real villain on the ship, however, is Mr. Boerhaave. If "Boerhaave!" isn't some 19th-century swear word, it should be. This guy gets his jollies by bullying others, like when he calls Adam Ewing "Mr. Quillcock," or when threatens to throw a crewmember to the sharks. Ewing observes that Boerhaave "takes pride in that very hatefulness which makes him notorious" (1.9.7). This kind of person is still around today. Just watch this CBS Sunday Morning piece on the "a-word" (viewer discretion somewhat advised), which lets us know that if you don't mind being called an a-word, then you probably are one.
While that's all terrible, what's really repugnant is his treatment of Rafael, a young novice sailor.
He repeatedly rapes him and torments him until he commits suicide. Rafael, afraid he's going to hell for what Boerhaave is doing to him, asks Ewing for advice, and Ewing tells him he is fine as long as he repents for his sins. Rafael later hangs himself.
Rafael's suicide sends Ewing on a crisis of faith. He berates himself for not seeing the signs of what was happening to Rafael, and wonders if he "[sent] that poor Innocent to Hell" (11.10.5) by making him think that death was a release. The fact that Rafael is around Ewing's son's age makes it even harder for him.
So, rampant bullying, institutionalized slavery, hypocritical Christians, anti-gay attitudes. Hmm, sounds like the Prophetess is a sign of things to come... and a shocking reminder of just how little things have changed in over a hundred years.