Basic Trope: An evil character cannot understand the motivation of good characters and thus fails to predict their actions.
Straight: Emperor Evulz does not believe in true altruism, so he is unprepared when Jesse sacrifices himself for a small village of people Jesse doesn't even know, and this leads to the Emperor's downfall.
Emperor Evulz has a psychological disorder that makes it impossible to empathize with other points of view. He genuinely believes that underneath their goody-goody exteriors, everyone else is just as self-centered and greedy as he is.
Emperor Evulz appears to have believed that Jesse wouldn't sacrifice himself, but it was actually a Batman Gambit specifically designed to make Jesse take the Heroic Sacrifice route, so that the Emperor's next plan can continue without interference.
But the Emperor didn't count on Jesse's sacrifice inspiring several ill-assorted villagers to take up the cause of freedom themselves and eventually defeat him. They were supposed to be permanently cowed by Jesse's horrible fate.
Evulz lives by an unusual moral code and is unable to comprehend more socially acceptable notions of good. The only reason Evulz thought it was moral was because it meant that Jesse was willing to take a risk "for once in his life".
Emperor Evulz is baffled by concepts like opening the door for people whose arms are full, not just throwing food wrappers on the sidewalk, petting small animals, and so forth.
Evulz has such difficulty comprehending good that he doesn't even understand the dictionary definition of "good".
Evuls hires a tutor to teach him how to be good, in an attempt to understand it. However, even after being explicitly instructed to Pet the Dog, Evulz shoots it anyway, and looks baffled when the tutor tries to explain what he did wrong.
Evulz understands some good actions and doesn't understand others.
Harile isn't technically good or evil, and as such cannot understand what motivates Jesse to constantly risk his life to help others when it doesn't even benefit Jesse.
Averted: Emperor Evulz has a normal understanding of how good people think and has a good idea of how they'd act in any given situation.
"We need to show how evil Emperor Evulz really is-let's make it so he doesn't understand/looks down on goodness
Lampshaded: "You just don't get it, do you, Emperor? Normal people don't think only of themselves, or of what personal gain they get from something."
Invoked: Jesse goes out of his way to help random people while he is a fugitive so that he wouldn't be where Evulz would expect him.
Exploited: Jesse sets up a Batman Gambit that relies on Emperor Evulz not thinking as a "good" person would.
Defied: "I am aware of the concept of altruism. I find it useful in my enemies, fools that they are."
Discussed: "I fear the master is setting himself up for a...disappointment, if he thinks that the rebels will not stick by their principles in a crisis."
Conversed: "Yep, Emperor Evulz fell into the old 'assume the hero is just as evil as I am' trap.
Emperor Evulz's inability to understand the viewpoint of "good" also extends to other viewpoints as well, making him an incompetent ruler who only sustains his throne through violence and fear. He has to constantly expand his empire as his mismanagement has ruined the economy and impoverished the land.
Emperor Evulz's inability to comprehend goodness has made it impossible for him find any chance of redemption; because he crossed the Moral Event Horizon, it doesn't even matter anyways, since he's unable to turn back and have a happy and normal life.
Emperor Evulz's inability to comprehend goodness made it impossible for him to appreciate any love or kindness towards him; as such, any victory will ultimately be hollow.
Reconstructed: While his narcissism and failure to understand selflessness is shown to make him a Bad Boss and a poor economist, he is still able to instigate a reign of terror productive enough to fund his evil schemes, and by appealing to people's selfish instincts, he builds up a powerful (if not particularly loyal) network of lackeys.
Played For Laughs: Emperor Evulz goes on a game show to win the MacGuffin prize that'll help him rule the world. But due to the categories revolving around petting dogs and diabetes-flavored subjects, he ends up losing and makes himself a laughingstock to the whole viewing world.
You can go Back to Evil Cannot Comprehend Good, though I can't imagine why you would want to. There's nothing in it for you, after all.