In Chapter 11, the nature of the ship and why it was burned remain a mystery. One might assume it was a merchant ship, but far too much weaponry was found on the ship for it to have been a merchant ship, including five cutlasses, which are short swords used by sailors, two cannons, and muskets. In addition, clasps and heavy chains were found along the hull, the sort of chains used on slave ships. Yet, a slave ship would not be heavily laden with weaponry. It is also clear that the ship was run aground and intentionally burned, but no one can see the reason why.

It is not until Chapter 20 that the mystery is resolved. The ship had been captained with Henry's ancestor, Captain Thomas Smith, the same ancestor responsible for the Smith family fortune. The ship, called the Seaflower, had been used in battle during King Philip's War (1675-1676), an unsuccessful effort of the Native Americans to drive English settlers out of New England. Captain Smith had then used the Seaflower to dispense with 180 Native Americans captured and enslaved during the war. Captain Smith had been unsuccessful selling the Native American slaves in the Caribbean and West Africa, so he sold them in Morocco. When he returned, he burned his ship.

As Thaddeus Baxter explains to Henry in Millinocket, Maine, no one knows exactly why Captain Smith burned his ship, but one can speculate he was so overwhelmed with guilt over his actions that he burned his ship and lived the rest of his life as a recluse. Another possibility is that he burned it because it was wrecked.