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Sometimes, the act of coming close to something or someone evil has a severe weakening effect on the character. This can be used as or a result of Detect Evil type abilities, but much less useful or pleasant for the character. Characters in denial about the power will often insist this is Definitely Just a Cold.
Other times, the evil entity may be invoking this deliberately; perhaps a character is possessed and it's making them physically ill, perhaps the Artifact of Doom is causing it, whatever. Discovering that there is actually evil behind the apparent illness can take a whole episode or few.
See also Allergic to Love, which is when someone is made physically ill by love. Good Hurts Evil is the inverse. Compare Achey Scars and the offensive version of Killing Intent. See also Cross-Melting Aura for a similar effect on holy items.
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Anime & Manga
The Brand of Sacrifice in Berserk on Guts and Casca will start bleeding or hurting if demons are near. If one of the Godhand is near, it gets even worse, as the evil they radiate will cause them to bleed profusely and rack them with serious pain, and if they get too close, the pain and blood loss will be enough to kill them. Guts could only get within about ten feet of Femto before being nearly overwhelmed by the pain during the Guardians of Desire arc. And as for Casca...she was much closer to Femto during what he did to her during the Eclipse. And she could not get away.
In Sorcerer On The Rocks, Gin Fizz (apparently) gets ill whenever they're in a bad place, like a seedy town full of whorehouses and casinos.
Akumetsu has Mary Kirishima aka 'Bloody Mary', a police officer who gets nose bleeds everytime she is around those who are evil.
Allen Walker of D.Gray-Man can tell humans from demons using his cursed left eye. But the once-human souls of the demons are not pretty to look at. "The world he sees is hell," as one of his comrades comments. The souls of level 4 demons are so corrupted they can't even be shown in the manga, and the mere sight makes Allen puke.
The Oracle from Spider Riders feels pain everytime an object dedicated to her, or an energy barrier she's created is destroyed.
Variation in A Certain Magical Index, Touma has the power to dispel anything related to magic or God (which seem to be interconnected). While he's not inherently bad, his name seems to come from Toma the Unbeliever (which makes sense with his power) and he's implied to be able to cancel out God. One of the nasty side effects for him is that healing magic can't work while he's in the target's proximity, and obviously, not on him either.
Sakura Wars TV: When she senses the coming of Crimson Miroku in episode 5, Iris comes down with a high fever and ends up screaming in agony when Crimson fully emerges.
Evil in the Lone Wolf series has pretty bad effects on anyone who isn't a supernatural embodiment of it such as the Darklords, and Lone Wolf himself is particularly sensitive to it. The Doomstones for example are the Kryptonite to his Superman. When facing extremely powerful and evil entities like Deathlord Ixiataaga, he needs the strongest psychic defense available just to survive this evil presence.
Harry Potter's scar hurts/burns any time Voldemort is close or feeling strong emotions.
In Garth Nix's Old Kingdom series, there is Charter Magic, which is used by the Old Kingdom, and Free Magic, which is mostly used by the bad guys. Free Magic is described as smelling "caustic"; a high concentration was once enough to make a character vomit, and some beings that channel Free Magic strongly will burn the flesh of Charter Magic users on contact.
In David EddingsMalloreon, C'nedra is taken over by Zandramas. Symptoms include hallucinations, depressive episodes, and lethargy. It takes Polgara a surprisingly long time to figure out what's going on.
This is also the cause of Arwen's problems toward the end of the third book/film.
Angels in I, Lucifer suffer from crippling agony known as "Angelic Pain". It literally hurts them to commit evil acts and corrupts their very essence. As you can imagine Lucifer's suffering is immense and technicallyself-inflicted.
In the Vampire Academy series, Rose has the ability to sense when Strigoi (a.k.a. the undead) are nearby (this is one of the effects of being "shadow-kissed", or having returned from the dead). While this ability proves useful in terms of self-defense, it manifests itself as severe nausea whenever Strigoi are in the area, which is extremely unpleasant and inconvenient, particularly when she's trying to actually fight the super-strong, super-fast, undead vampires.
One of the Torchwood novels has Jack unable to investigate a certain location in Cardiff for decades due to becoming severely ill whenever he tries to go near it. There naturally turns out to be something rotten underfoot there.
The Heirs Of Alexandria series has "witch smellers", who literally smell dark magic. And sneeze, if it's powerful enough. Detecting useful details takes practice and training, though.
In Charmed one cupid gets hurt every time the demon of hate unmakes a relationship he put together
Star Trek: The Next Generation: In the episode "The Battle", Picard starts having headaches when the Enterprise rendezvous with a Ferengi ship who are "gifting" him his old (and thought lost) ship, the U.S.S. Stargazer. The Ferengi captian is secretly the father of the ship captian that Picard defeated with the Stargazer in the "Battle of Maxia". He has a spooky glowing orb of doom. You can see where this is going...
One of Duncan's immortal friends from the Highlander tv series would sneeze and have cold symptoms whenever another immortal was near. It was definitely not useful to him, (and he repeatedly cursed it) since all immortals can feel the presence of each other anyway when they get close enough.
Babylon 5: Both Delenn and Talia Winters have strong negative reactions to the presence of the Shadows accompanying Morden.
In Ōkami, Ammy takes damage and loses ink when she's in cursed areas (and ridiculously fast, too, so you can't skirt into said zones for Sequence Breaking).
In Xenosaga, certain people are capable of contacting U-Do, the mysterious existence which hangs as a boogeyman over most of the game. This contact causes their consciousness to break down with fear, leading to fainting spells and eventually a coma and death. Shion's mother Aoi was hospitalized with this "illness." When Shion starts getting the same fainting spells, she insists it's just fatigue.
The atmosphere of Dark Aether in Metroid Prime 2: Echoes is damaging to anything not from that realm. As such, Samus takes constant damage in Dark Aether when not within the field of a light crystal. This being Metroid, she eventually gets upgraded suits that massively decrease and eventually outright negate the effect.
Played straight and subverted (or averted) in Sailor Nothing. The way Himei detects the birth of Yamiko is through near-debilitating headaches. However, she can't tell if she's near one, even if it's in front of her, after it's been born.
Ears: Imagine the worst thing that's ever happened to you. Now imagine that it's not just happening to you, but to everyone you care about. That's kind of what evil feels like. Chief:Blaa! That sounds unbearable! Why would anyone want to be a paladin? Ears:So others don't have to.
Sluggy Freelance: The Goddess of Goodness is pretty weak when awakened in the middle of the Dimension of Pain, because there's very little goodness around in there.