"So that was Mrs. Lundegaard on the floor in there. And I guess that was your accomplice in the wood chipper. And those three people in Brainerd. And for what? For a little bit of money. There's more to life than a little money, you know. Don't you know that? And here ya are, and it's a beautiful day. Well, I just don't understand it."
Bob and Alice are being terrorized by Doctor Deathmurderkill. He has hunted them, attacked them, and nearly gotten them killed on several occasions. Bob is convinced that Dr. DMK has kicked the dog more than enough times to warrant fighting back with lethal force. Alice, however, insists that he must have a good reason, or maybe that it's all just a big misunderstanding. Despite any evidence to the contrary, Alice refuses to believe that he can actually be 'evil'. After all, no one's that heartless, right?
This trope is, in its essence, a character who refuses to believe that someone could simply be evil for its own sake. If this character can talk things out with the villain than their motive will come out and together they can find a better solution, (perhaps after pounding them into submission). It doesn't occur to them that there might not be a motive to discover.
Whether Alice is right or not depends on the work's placement on the Sliding Scale of Idealism vs. Cynicism. In an idealistic show, this attitude could very possibly lead to a Heel-Face Turn. In a cynical one, expect her death to be the very thing to push the villain over the Moral Event Horizon.
This trope is usually limited to the very naive and very young, or the very old and war-weary, who've grown tired of the "black and white, us vs. them" attitudes of those around them.
Note: Be careful not to just stick this trope onto any pacifistic characters, whether technical, actual, or martial. The tropes are related, but one does not automatically imply the other.
Compare Stupid Good, The Pollyanna, White and Gray Morality. Contrast Evil Cannot Comprehend Good, Complete Monster, This Is Unforgivable.
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Anime and Manga
Seiichiro Kitano from Angel Densetsu is always the target of thugs or other people who try to attack him because he looks like a monstrous, evil devil or something like that. Kitano is so naive and good that he never has bad thoughts and has no idea why would people do bad things and he cannot recognize bad actions very well. When people attack him, he believes that he did something bad to them that made them angry, that's why he lets them keep hitting him. And if (it happens rarely) he recognizes bad actions (which he mostly misinterprets), he tries to stop them.
This is one of Danny's major flaws in Cats Don't Dance. He proves to be too naive to realize how evil Darla Dimple really is. This comes back to bite him in the butt when she sabotages his an the other animals' audition for movie studio mogul, L.B. Mammoth, initially thinking she wanted to help.
Hiccup in How to Train Your Dragon 2 is insistent on trying to reason with Drago despite his father's warnings. Later events transpire to teach him that, unfortunately, some people just can't be reasoned with.
Films — Live-Action
Star Wars: The Jedi Order suffers from this problem, and the Star Wars Expanded Universe has shown again and again that for a group that acts as champions of good, the Jedi Order has absolutely no understanding of the dark side. Justified since many of them refused to so much as study the Sith or the Dark Side, believing that even trying to understand evil would lead them to fall.
In The Dark Knight, Bruce hits a dead end trying to understand and figure out the motives behind The Joker; it's with a little help from Alfred that he comes to accept that there is no why behind The Joker, hejustis.
In Star Trek Into Darkness, the heroes had a lot of trouble wrapping their heads around the fact that Admiral Marcus was a corrupt traitor.
Schindler's List: For a long time Oskar Schindler seems to think that Amon Goeth would be a much better person if there weren't a war going on, which Schindler thinks brings out the worst in people. He's incredulous that Goeth could enjoy killing people until Stern confirms the number of atrocities that the Nazi Captain has already committed.
Harry Potter: Dumbledore has shown that he can understand quite a bit about Lord Voldemort. However, it turns out that Dumbledore was unable to figure out that Voldemort hid one of his Horcruxes in the Room of Requirement. Why? Because Dumbledore was a model student who never cheated and hence had no need to use the room to hide anything. Harry, however, was certainly not a model student, he cheated a couple of times, and he used that room, so he could figure it out.
In Death series: Dr. Mira in Midnight in Death is unable to find out why David Palmer is such a Complete Monster. Eve Dallas is unable to find out why her own mother is a Complete Monster in New York To Dallas.
In The Silmarillion, it is said that the Valar don't understand Morgoth's evil, and explicitly didn't understand it was incurable. The most obvious manifestation of this failure is when Morgoth was imprisoned for millenia after his first rebellion; the Valar ask him if he has repented, and believe him when he says he has because it doesn't occur to them that he could be lying. Cue Morgoth plunging the world into darkness yet again.
Sisterhood Series by Fern Michaels: The Vigilantes have shown that they cannot understand why people like the Monarch HMO in Payback, Karl Woodley in The Jury, and Maxwell Zenowicz in Fast Track are such evil people.
Early in the Discworld series, Granny Weatherwax of all people. The Duchess mocked Granny's attempt to make her have a Heel Realization, claiming that Granny was naive for believing that all people really are good deep down. One of Granny's core philosophies is basically "Once you truly comprehend good, you can't choose to be evil." A philosophy that she started vocalizing after her encounter with The Duchess.
In the Warrior Cats series, when Bluestar's suffering from dementia and is absolutely convinced that WindClan is stealing prey, she won't listen to Fireheart when he gives her evidence that a dog has been killing the prey. She tells him that he's a good and noble warrior, so he can't comprehend that other cats would have morals any less pristine than his own. He especially thinks this comment is odd, since he was the one that exposed Tigerclaw as a traitor and murderer.
Annabeth Chase from Rick Riordan's Percy Jackson and the Olympians refuses to believe her former best friend Luke Castellan is evil, even after he attempts to kill her several times throughout the series, insisting that he is just being manipulated by the titans and is a victim.
In the Star Trek: The Original Series episode "The Savage Curtain", Surak, Spock, and President Lincoln have a hard time understanding the motives and actions of the opposing "evil" side. Only Kirk seems to have a grasp of their potential for deceptiveness and duplicity.
The Highs in Red Dwarf when presented with the Lows.
High Kryten: The poor wretch, he has a faulty gun! He's accidentally shot me five times! Oh, how I love him!
The Mentiads in the serial "The Pirate Planet" state this as the reason they had not deposed the Captain prior to the Doctor's arrival. They are incapable of understanding why he does what he does, and are unable to properly work against him as a result.
In the revival series, there's a downplayed example. The Doctor can't work out why the Weeping Angels' method of attacking Amy involves needlessly tipping her off in advance. He's briefly dumbstruck when he finds out that they're just doing it to terrorize her.
Gwen: Why? Why would you wake up one morning and decide that this is what you want to do?
The villain: Because it made me happy.
In Fargo, the murderous liar Lester is in conversation with his brother, who grasps to understand him and states, "There's just... something missing."
In the lore of Warcraft, this is what happened with Sargeras, the creator and leader of the Burning Legion. Originally belonging to a race of god-like beings called the Titans, he and his kind traveled throughout the cosmos to bring order to worlds; they were so powerful they defeated the Old Gods, the Eldritch Abominations of Azeroth, and created the dragons to become the world's stewards. While defeating and imprisoning the demons of the Twisting Nether, their evil caused Sargeras to question the Titans' quest for order. He was driven into depression after witnessing the chaos wrought by the demons, especially after defeating the vampiric Nathrezim, whose manipulative bastardry on various worlds affected him deeply. Eventually, he went completely off the rails with the belief that the Titans' quest for order was essentially wrong, given that he saw the Universe as intrinsically chaotic and evil. The last the Titans saw him, Sargeras had freed the demons he had personally previously imprisoned, made them a part of his army, and sent his Burning Legion to bring war upon the Universe, putting into action the corruption of the Draenei and Orcs, the birth of the Lich King, and the multiple near-destruction of Azeroth itself. An example of Good Cannot Comprehend Evil taken to epic proportions.
A defector from an evil organization thought that she had hidden families safely on a remote world, because she "couldn't imagine" the organization's leader coming after them. Shepard says "That's what evil counts on..."
After discovering the various atrocities at Sanctuary, Ash (who is by no means a naive character), says she truly cannot understand what motivated it. She also says that she's actually glad she can't, as it makes her feel human.
Knights of the Old Republic and its sequel Knights Of The Old Republic II: The Sith Lords show the Jedi to be very ignorant of the Sith order and the motives of those who turn to the dark side. In particular, Darth Revan was able to convert so many Jedi to his cause not only because of this trope, but also because he was a notable aversion of Evil Cannot Comprehend Good. Revan understood the order and its flaws far too well, exploiting them to deadly effect.
Comes up again in Star Wars: The Old Republic, the Jedi order is apparently blind to the massive corruption in the Republic and a large number of dark Jedi, Sith aligned and otherwise, in their own ranks.
Treasure of the Rudra takes this almost to the point of Running Gag. Surlent assumes that everyone he meets is as honest and compassionate as he is, which leads to him trusting the wrong people and getting screwed as a result of it several times throughout his scenario.
In the intro chapter of Bravely Default, the Wind Vestal Agnés is being hunted by soldiers from the Duchy of Eternia. At first she is willing to surrender to them to stop their attack on the city of Caldisla, assuming "they are men, not monsters". When she goes to turn herself in accompanied by Tiz, she meets the leaders of the assault. When they tell her how they want to beat her to within an inch of her life, then heal her just so then can do it again over and over, she realizes that they are, in fact, monsters. So begins the game's first boss fight.
Fenthick in Neverwinter Nights is another example; he is so good that he simply cannot conceive of the possibility that anyone else could be evil. It comes back to bite him.
The Batman has one episode where Batman actually tries to make sense of The Joker. By the end, it is safe to say that Batman figures out that doing this is an exercise of futility and madness.