Biography
The villain has developed a devious plot that is prepared for anything that the hero might do — except for one glaring flaw. For some reason, the villain has not considered the possibility of a Heroic Sacrifice. After all, you'd never catch him throwing his life away to save a bunch of lazy, ungrateful civilians who don't care about anybody except themselves. Heck, even saving your True Companions comes after saving your own life. Only an idiot would throw his life away like that—and only because he didn't realize how much more profitable saving it would be.
Too bad for these villains that Machiavelli Was Wrong, for they cannot understand the concept of goodness or generosity because there is no guaranteed return on that investment. Why do they have so much trouble understanding good behavior?
Our Hero goes and makes the Heroic Sacrifice anyway, thereby ruining the villain's plan with a Didn't See That Coming that a more cunning villain really should have seen coming. This is one of the ways those with Honor Before Reason can continue to defeat the Big Bad. This is a major problem for villains who really believe they aren't so different, and think heroes could have used their powers for Evil, as opposed to villains who are just screwing with the Hero's head.
Occasionally, greater justification is provided by having a hero who the villain knows is a Jerkass and the Anti-Hero decides to redeem himself at the critical moment, or the villain will meet a hero who decides to Turn the Other Cheek instead of fighting back. An alternative version involves the Hero giving in to the villain's manipulative demands, agreeing that, yes, We Can Rule Together (usually to the "horror" of his sidekicks, Love Interest, and True Companions) as a ruse to defeat the villain. The villain falls for it because it's what he'd have done if the situations were reversed.
The inability to comprehend good altruistic behavior (especially when it results in punishment) is a common trait in cynics, Straw Nihilists, Corrupt Corporate Executives, Social Darwinists, Knight Templars, and sociopaths.
Contrast It's All About Me, when the villain expects the hero to behave not selfishly, but generously toward him. Contrast Virtue Is Weakness, which is similar in practice but different in principle: a villain does understand noble qualities like love, friendship, and altruism... but holds them in disdain, and believes themselves "stronger" by not holding onto them. When the trope is Evil Cannot Comprehend Good, the villain can't understand why the hero saved him from falling; in It's All About Me, the villain can't understand why the hero insists on arresting him after. It can get a little fuzzy when the character decides to be generous: did he murder his son's romantic rival because he didn't realize his son would hate it — this trope — or because he was so caught up in the notion of his own generosity that he didn't care what his son thought—It's All About Me?
A Super-Trope to Beware the Honest Ones and Sub-Trope of Wrong Assumption. Contrast Good Is Old-Fashioned, Silly Rabbit, Idealism Is for Kids!, and the Inverted Trope of Good Cannot Comprehend Evil. Compare Blue-and-Orange Morality. Often involves Psychological Projection. When someone evil is capable of understanding or admiring good, it may lead to Sympathy for the Hero. If the villain thinks he is the good guy and is baffled at the heroes wanting to stop him, it's because he's Obliviously Evil. Curious Qualms of Conscience could be similar to a milder form—characters who don't understand the good and the conscience within themselves.