In the Evil (bad) ending of Dishonored, Samuel fires a flare to alert the guards, saying that Corvo is not so different to the antagonists. Why did he do that, knowing Corvo is the only hope to find and save Emily?
In my humble opinion it's simply this: to get the "High Chaos" ending you have to have pretty much killed everything in your path, and this has been eating away at Samuel (whose comments become increasingly sour as you progress through the missions even before the end).
By the time Samuel has delivered Corvo to Kingsparrow Island, the long boat journey has forced him to ask himself: will the young empress be any better off in the hands of this mass murderer? And, having decided that things could only be worse with Corvo hovering over the throne, Samuel tries to throw him to the wolves.