Let's get one thing crystal clear before we do any further: There isn't an actual ending to this book since it's only the first volume in a two-volume series. So if you're looking for the typical payoff of a satisfying ending, get thee to the nearest library for the second volume—because you're not going to find things wrapped up neatly in this one.
That said, what you have instead is a really exciting cliffhanger because Dr. Trefusis and Octavian have just started crossing the Channel from Roxbury to Boston.
No big whoop? Oh, but it is. You see, the Brits now hold Boston, which means that our Batman and Robin-esque duo (we can't say which is which though) have just traded one hostile territory (The College of Lucidity and Mr. Sharpe) for another. What this means for Octavian's quest for freedom from slavery, however, remains to be seen. As he points out:
I thought on the word freedom, and could picture nothing that it might be, beyond freedom to die; I knew not what the hours held; nor whether I would hang, nor fight, nor what man I would be, nor what woman I would take to wife; nor what would be the fate of this nation, birthing like a Caesar, tearing tis mother midst blood and travail. (4.12.163)
He's only seen black slaves "freed" through actual death, so no wonder he's at a loss as to what he should imagine or hope for. However, he does know one important thing: "We left the Patriots behind us" (4.12.163). This is super important, because leaving the Patriots behind means Octavian and Dr. Trefusis are willing to switch sides. Is that an act of betrayal? Are they traitors? Can you be a traitor when your nation betrays you first? Is America even your nation if you're a slave in the first place? So many questions.
For what it's worth, the second volume is titled The Astonishing Life of Octavian Nothing, Traitor to the Nation, Volume II: The Kingdom on the Waves. It doesn't tell us much, but it leaves us with a hunch that this swim Octavian and Dr. Trefusis are taking as Volume 1 ends won't be their last.