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Pokémon in general. A lot of them must have pocket dimensions inside them to hold all that water/rock/webbing/snow/acid/etc. And, of course, there's the logistics behind Fire and Electric Pokémon not hurting themselves...
In the newer games, this is somewhat addressed as Fire-type mons can't be burned, Poison-types cannot be poisoned and Ice-types can't be frozen. Also, Electric-types can't be paralyzed by Electric moves, but can be by moves such as Stun Spore and Body Slam (up until Gen VI, where they can no longer be paralyzed by the latter either).
The only TM that can be taught to every single Pokémon (except Magikarp, Smeargle and Unown) is the move Toxic, which means that nearly every single species of Pokémon - including the Ridiculously Cute Critters like Jigglypuff, Pichu and Skitty - can produce highly poisonous substances. Which makes sense for most of them, as every living creature produces waste products in their bodies (now, Pokemon like Magnemite or Porygon, well...).
Ditto and Mew can physically transform into any other species of Pokémon, but when turning into something like Wailord or Groudon they surely have a way to defeat the whole Conservation of Mass thing.
Mario, when properly empowered, can throw fireballs (and ice balls) and not be burned/frostbitten by them, but is harmed by other fire sources.
The times in which a power Mega Man acquires is noticeably different from its source (Top Spin and Charge Kick), it's because he doesn't have wheels on his feet and must adapt the move. Further, he must have a built-in replicator to construct the ammo for those weapons that are physical in nature (such as the Metal Blade or Needle Cannon).
This is also the case with Mega Man X and Axl. They can't fully replicate the weapons as used by the bosses and adapt them as well. Although in X's case, once he gets the hardware upgrade for his X-Buster, he can charge the special weapons up and do things that the bosses couldn't do themselves.
Also, the characters must have an extremely high tolerance to sudden changes in temperature and other forces to function in all the environments they do. The first X series game has a moment where you destroy an enemy in an airport's control tower, with the force of the blast blowing out all the windows in this fairly large room. Considering you'll destroy many more of this type in the game, you can imagine the kind of forces that X is bombarded with during the games.
Sonic the Hedgehog's immunity to G-forces are a no-brainer, but he's also managed to fall from space at least twice without any significant injury. He can not only breathe at supersonic speeds, but also, again, in the total vacuum of space. Can't breathe underwater, though, because... huh?
In Sonic the Comic he was affected by friction, as it stated he was a brown hedgehog and breaking the speed of sound changed his quills blue.
It was also a problem with his shoes; in a comic printed in one of the strategy guides, it opens with Sonic trying out his friction-resistant red-and-white shoes, which his uncle invented after burning through several previous pairs.
In Adventures of Sonic the Hedgehog, it's shown that he is reliant on his shoes to be able to run that fast without burning his feet. Naturally, they get stolen for an episode forcing him to do without.
Canon said that at the end of Sonic 2, when Sonic was re-entering on Earth, he was Super Sonic then. (The first seconds of Sonic 3 show Sonic going Super... for a while.) Perhaps it was done to avoid scaring everyone. "Sorry, you saved the world, but because you didn't get the seven emeralds you're dead."
Maybe only in the Archie comic, but the rings are supposed to provide energy. It could well be inferred that Sonic offsets his need to be a Big Eater by having a lot of rings. While this might mean he's also effectively an energy leech, most of his allies seem to be too. On at least the level needed to create a personal protection field.
In the Sonic Sat AM cartoon, the rings served the same purpose, and he could only acquire one every 12 hours (thus limiting the flow of Phlebotinum and preventing him from using his super-speed powers to become a Sprinting Brick.
It's also pretty obvious that Tails has not only some kind of healing ability, but an anchoring one as well, explaining why his tails stay attached to him whenever he flies. Likewise, his tails must also be very strong to achieve flight (with Sonic Heroes having him carry himself, Sonic and Knuckles simultaneously) as various games allow him to attack with just his tails.
There's one notable aversion throughout the series: None of the characters have super-acceleration. The very shortest amount of time it takes a character to reach full speed is just over two seconds. As the series went on, the characters became faster, but didn't accelerate any better, so it can take over ten seconds for them to reach full speed.
Lampshaded when the Space Pirates try to reverse-engineer Samus's powers. They manage to clone her basic weaponry but abandoned the Morph Ball research due to... let's just say "unknotting a pretzel" and move on.note "Science Team is attempting to reverse-engineer Samus Aran's arsenal, based off of data acquired from her assaults on our forces. Progress is slow, but steady. Command would dearly enjoy turning Aran's weapons against her. We believe we can implement Beam weapon prototypes in three cycles. Aran's Power Suit technology remains a mystery, especially the curious Morph Ball function. All attempts at duplicating it have ended in disaster: four test subjects were horribly broken and twisted when they engaged our Morph Ball prototypes. Science Team wisely decided to move on afterward."
Certain depictions, Super Smash Bros., the e-manga, and Prime for example, solve the problem of how Samus jumps with all that armor on by showing that she has jump-jet assistance.
Rolling around in the Morph Ball also requires Samus to be immune to motion sickness, not to mention impact trauma when she lands, boosts into walls or is hit by enemies.
Prime (again) shows that the Morph Ball turns Samus into a small cloud of energy while engaged — the two halves of the sphere have a seam between them you can see right through if you roll the ball the right way and hold still. Presumably "Space Pirates who saw the Morph Ball hold still long enough to realize this" and "Space Pirates whose lives didn't end thirty seconds later" are mutually exclusive groups.
Recurring series villain Ridley is a Giant Flyer, with all the logic problems that implies. Prime mitigated it somewhat by giving him forcefield wings, which would essentially be massless, aside from the physical parts by which they are generated.
Metroid Prime 2: Echoes: The Luminoth tried to weaponize the toxic nature of "Dark Aether" against the Ing... except they are perfectly fine in their environment so the weapon did nothing to them. However the Ing have the opposite problem with our world (so a light gun was invented) and as such the Ing can't enter "Light Aether". To work around this they can (and often do) possess corpses, machines and animals to do the attacking for them.
In Quake, the Ring of Shadows power-up makes your character invisible, but lacks the appropriate secondary power. End result? You appear to others as a pair of small floating eyes.
In the Condemned games, protagonist Ethan Thomas has the primary superpower of super shouting. Sadly, he doesn't find out about it until two thirds of the way through the second game, and doesn't learn how to use it until the last level. Thankfully, the super-dense bone structure that allows him to produce the necessary sonic vibrations also gives Nigh-Invulnerability.
Halo... insofar as the Mjolnir armor can be considered a "super power". It's mentioned in the books that the Spartans are the only human beings capable of wearing it, because their enhanced durability (particularly their harder bones) is what allows them to survive the armor's incredible strength. An ordinary human was killed when testing the armor because even the slightest movement shattered his bones.
To go into detail, the "normey" tried to move, and broke something. He then spasmed due to the pain, and broke something else. This pretty much repeated until death. The liquid-crystal matrix that was used to enhance the strength of the user could not actually be scaled back for the existing models, and since the suits were being designed for the Spartans anyway, no one bothered re-engineering the suits for normal soldiers.
The Pyro from Team Fortress 2. The only reason it can run and fire his/her flamethrower is that it wears a fireproof suit.
Rumia, a darkness-generating character from Touhou, cannot see through her own cloak of darkness, which results in her aimless wandering being constantly interrupted by collision with trees.
Not even lame powers are immune to this trope. Rinnosuke has the power to identify the name and purpose of any object, but that doesn't mean he understands its actual function. He deduced a Game Boy that had fallen through the Barrier was for the purpose of destroying large amounts of enemies, but is unaware of the existence of video games and so concluded that it was a powerful weapon.
Alex Mercer from Prototype, much like Mystique, is technically naked all the time. His "clothes" are just shapeshifted tissue that are still part of his body. This explains why none of his footwear is instantly ruined when he jumps off a skyscraper or heck, even when he's on a stroll considering he actually weighs at least a ton due to Shapeshifter Baggage. This also handily justifies why his clothes are never ruined; presumably he automatically regenerates any damage to them thanks to his Healing Factor.
Being a wad of nothing but biomass also explains how Mercer can hip-drop a tank from the top of a skyscraper and walk away uninjured - he had no bones to break or organs to rupture.
Similarly, Mercer is a giant wad of biomass, and given some of the powers he can pull off (such as turning one of his arms into a gigantic blade or coating himself in thick armor), it's got to be dense. This is backed up by how glass cracks under his feet when he runs up the side of a building, and how he instantly sinks to the bottom of any body of water he falls in (only to leap back out when he touches the bottom).
Some of this in inFAMOUS. Cole's electricity powers must also come with some control over magnetism for him to decrease his falling speed and jump off of skyscrapers only to land without breaking anything - it's mentioned explicitly that being able to jump off buildings is a part of his powers, but how it relates to electricity is up to conjecture. More obviously, Kessler's final power once he fully evolved as a Conduit was the ability to travel into the past one time, but likely thanks to this trope, he's immune to Temporal Paradox and freely alters his past life with no side-effects to himself.
Cole's free running and climbing abilities aren't from the blast but come from his time doing parkour which he mentions in the sewer sections.
Also, the mere act of shooting lightning bolts means Cole would have to be immune to flashbangs, since realistically he would be getting hit by the equivalent of one every time he fired a lightning bolt. He'd also have to have a way to withstand extremely high temperatures and x-ray radiation since lightning generates extremely large amounts of both.
The lack of certain secondary powers is mentioned in some smaller conversations, mainly the fact that he can't turn the electricity off, and as a result can't go into water without zapping everyone else in it and draining himself, and can't hold a gun without it exploding in his hands when the electricity "cooks" the gunpowder. At one point, when Zeke mentions good news, Cole snarks, "They built a car I can sit in without blowing it up?"
This is used at several points in both games where you can destroy enemy machine guns simply by holding them and also explains why you can't just take a mook's gun and shoot him with it.
Likewise in the second game after rescuing Kuo who now has ice powers, she lacks sufficient control over her powers and accidentally freezes part of Cole's face when she touches it. While she gets better, the Vermaak 88 take this even further and slowly turn into giant ice monsters called Titans. This is because their powers were forcibly grafted on and they don't have any of the powers to stop the ice from giving them frostbite, freezing whole limbs, or other issues. While it doesn't kill them it drives them mad with constant anguish.
This trope is what makes Shirou and Archer from Fate/stay night so dangerous. Sure he is able to replicate swords, even Noble Phantasm swords, but they are weaker imitations of the original. However, he can also replicate the skills of the original's wielder throught the weapon's memory, allowing him to draw on the skills of countless swordsman, including heroic spirits. Gilgamesh has the similar power of summoning the prototypes of Noble Phantasms, but without the ability to wield them effectively, he loses in his fight with Shirou despite Shirou using weaker versions of Gilgamesh's own weapons.
In Metal Gear Solid, due to an inability to "turn off" his telepathic powers, Psycho Mantis wears a gas mask in order to block out the constant flood of thoughts he receives from others. How a gas mask keeps out people's thoughts is beyond me, but steel helmets worked for Magneto...
In Metal Gear Solid 3, Volgin the Psycho Electro also has superhuman strength. The strength allows him to punch holes in solid concrete, but it's also required for another of his favorite moves: using his electricity to fire bullets held between his fingers. Without super-strong hands, the kickback would break his fingers.
In Metal Gear Rising: Revengeance, a codec conversation has Doktor declare that further upgrades to the special eyepatch Raiden is using would be pointless because the human brain would not be able to use any additional resolution it might give him. This is also the rationale behind the majority of cyborgs opting for full-body conversions; a super-strong and super-durable robot arm is no use whatsoever if it's attached to a squishy human torso.
The Soul Series makes a case for a perfectly mundane character laking a Required Secondary Skill: while Cassandra is plenty proficient with the weapons she "borrows" from her sister, she doesn't know how to take care of them. Not normally an issue, except during her ending of Soul Calibur 3 where her sword breaks after being used to shatter Soul Edge, and Sophitia catches her trying to hide it after a bad patch job and sends her straight to the forge to fix it properly. Cut to Cassandra having a sobbing fit on the forge floor, sword still broken, wailing that she doesn't know how to fix it.
In Bioshock, the Little Sisters have the ability to heal very quickly due to the sea slug in them... but quickly does not equal correctly. One audio diary tells about how one Little Sister broke her legs, and they healed at awkward angles. In order to fix them, she had to keep having her legs broken until they were in the correct position. And what's worse is that Little Sisters aren't immune to pain.
In the diary concerning the Telekinesis plasmid, Dr. Suchong mentions that it can't be used to do a Bullet Catch - not because of the plasmid's deficiency, mind, but the user's reaction time.
On that pain thing... they tried making the Little Sisters incapable of feeling pain, but that actually made things worse, since they wouldn't realize when something was injuring them.
The main characters of the games aren't immune to their own plasmids/vigors. This doesn't cause you any harm, but it makes for some interesting Body Horror; fire abilities char the skin of your hands, ice abilities cause visible frostbite, and you don't want to know about Insect Swarm.
In Dark Forces II: Jedi Knight, there is a little of aversion of this in play when using the Force Speed and Force Jump powers. Using either at its highest setting causes a little damage to the player upon running into something or landing on a surface equal or lower than the one from which he or she jumped. If a player tweaks the powers outside the game (which is quite easy), Force Speed can easily mean death when running into stair steps at top speed, and Force Jump can be a great way to get higher, but the fall back down is a killer. The sequels apparently address this by increasing the distance characters can fall without taking damage as a side feature of their increasing Force Jump skill.
Deus Ex: Human Revolution has two separate upgrades: the Icarus Landing System (sort of a fancy auto-deploying electromagnetic parachute) and the High Jump (see previous two words). Problem with the latter is, it often propels you higher than the minimum distance required to hurt you upon landing; a surface just a couple feet lower than the one you started on makes a big enough difference. So, get the jump before the Icarus, and be prepared to spend a lot of time waiting for your health to recharge so as to avoid nickel-and-diming yourself to death.
The use of cybernetic implants in general is also explored. In real life, cybernetics that are married to biological tissue face issues of immune system rejection and the buildup of glial tissue that results in the device not working. As a result, anyone in the setting who uses augmentations must take regular doses of the drug Neuropozyne or their own bodies will reject their augs. The fact that Adam Jensen doesn't have this rejection issue is an important plot point; he is the "Patient X" that Megan Reed was referencing as having the genetic ability to allow cheap and sustainable augmentations available for all of humanity, and the breakthrough was what triggered the Illuminati's attack on Sarif Industries because of fears that human augmentation would go out of their control.
The water breathing potion in Terraria makes it so that you drown in the air while it has its effect. However, if you wear a fish bowl on your head, you can go in and out of water just fine.
A lot of the flavor text in Starcraft II is dedicated to explaining the secondary powers of the units.
Viking pilots must be able to bend quickly or the machine will crush them during the air to ground transformation sequence, and most pilots die because of this during their first battle.
Ghosts can read the minds of others, but can't block other ghosts from reading their thoughts.
Almost all the Dominion's forces have been "neural resocialized" (read, brainwashed) so they are suicidally complacent (most of the army is former criminals).
The Hydralisk has several thousand more muscles in its large head than the entire human body. Each is needed to fire their spikes. which can pierce future tank armor.
Many of the Zerg strains you get in Heart of the Swarm show that the Zerg created them by placing them in various hostile places (such as versions of roaches that can slow down enemies or Banelings that can climb up walls), then waited for natural selection to kick. It is mentioned and shown that a LOT of Zerg died before they got any useful genetic material. The mass amount of death didn't matter if even a single scrap of genetic material that was an improvement was gained.
As well as being armed with a portal gun, Chell in Portal is fitted with a pair of legs springs that allow her to survive falls from any height. According to the commentary, the developers added these because playtesters complained about the lack of realism. Even though the leg springs couldn't possibly account for all the issues with surviving falls, the complaints stopped.
In Command & Conquer 3: Tiberium Wars the flamethrower-using Black Hand aren't immune to hostile fire attacks, because while their armor is flame retardant, they're spraying high-energy plasma at each other with sufficient power to melt tank armor.
Discussed in Mass Effect with regard to biotics, who can manipulate mass effect fields to lift, throw, warp, or block things. This is done because they have nodes of element zero in their bodies that are activated by electricity from the nervous system and produce mass effect fields. The asari are the only species that can naturally do this on any significant scale; every other species must have implants to strengthen and control their powers, allowing their biotics to actually become useful, as most species' bodies can't generate electrical fields like that. There's also the problem of energy, as using biotics uses a significant amount of it. Because of this, biotics have a significantly higher required calorie intake than ordinary people (twice as many calories are allotted to biotic soldiers as compared to regular ones, for example) and often have to stop to eat and rest after extended use of their powers.
Shepard in Mass Effect 2 onwards. The M-300 Claymore shotgun and the M-98 Widow sniper both generate so much recoil force that they shatter the bones of a normal human's arm. Normally, the shotgun is only seen in the hands of a genetically-modified super-Krogan and the sniper rifle in the hands of a Geth platform. Shepard's cybernetic upgrades that s/he receives in the beginning of Mass Effect 2 are what allow her/him to fire these weapons. Though the makers of the weapons managed to dial back the recoil so that anyone can use it without making their arm a pile of broken calcium.
The third game reveals that the asari's biotic power isn't natural either. The Protheans uplifted them in the hopes that the asari would lead the other races against the Reapers. Instead, the asari squandered their gifts to lord it over everyone else. Javik, the last Prothean, will call them out on their wasted potential.
Tribes gives every player a device that renders their suit frictionless, allowing them to "ski" around the stage at high speed. Activating this system also causes every jet of their jetpack to start idling, explaining how they manage to stay upright.
In Syndicate (2012), the infobank entry for liquid shields says that they can withstand even 105mm rounds, but the concussive force transferred pastes the shieldbearer.
The "Phase-" powers that Sirens can use in Borderlands have certain specific physical limitations. Lilith's Phasewalk power, for example, shifts her into an alternate dimension, where she can't be seen or attacked - being literally immune to energy from our dimension, both electromagnetic and kinetic. At the same time, while Phasewalking, Lilith can't operate objects, fire weapons, or jump, because she can't exert energy against objects in our dimension either. Maya's Phaselock power lets her lift and trap enemies in the same dimension, but she can't do it to massive objects like Constructors or other large machines; instead the force exerted by the Phaselock does tremendous damage to the target. Angel's ability to Phaseshift lets her take control of Hyperion machinery, but she can't simply take control of any device; she can only hack networked Hyperion machinery, and anything not made by Hyperion is inaccessible. This is why Handsome Jack needs to trick the player into installing a Hyperion device into the shield system in Sanctuary, and later on, Angel has to "coerce" Hyperion engineers controlling the lunar deployment systems to launch a Fast Travel Beacon by shutting off their air supply.
In the Dragonborn DLC you meet a mage who wants to fly. He successfully casts the spell, rockets into the air... than crashes back onto the ground. Turns out just because you can get in the air doesn't mean you can stay in the air, and nothing is cushioning you from the ground.
The ability to use the Shouts for normal people require years upon years of study, as the words must be spoken with meaning in the dragon tongue. Without the understanding of the words, even if a normal human can utter the words it would generate no effect. The reason the Dragonborn is unique is that they are born with the necessary secondary powers (namely, the ability to absorb another dragon's soul) to understand the meaning behind the words.
Similarly, Morrowind has the Scrolls of Icarian Flight, which allow the user to jump massive distances. However, unless the character has a slowfall or levitation spell prepared there is nothing to prevent them from fatally crashing to the ground. You find these scrolls on the corpse of their inventor, who falls from the sky after not taking the necessary precautions.
Having an absurdly high Acrobatic level, as Icarian Flight gives you, actually does grant you the required secondary power of protecting against falling damage. The problem with the Scrolls is that they wear off before you land...
Kirby's Epic Yarn has a small example. Kirby cannot use his famous sucking powers after he becomes a piece of yarn. While he can suck air in, Kirby's string body is flat and completely open, so the air just goes straight through him.
On the other hand, he can transform into a parachute to slow his fall.
The Power Bracelet/Power Gloves is a recurring item in The Legend of Zelda that allows Link to lift or move large objects. Twilight Princess does not contain this item, but the Iron Boots have a similar effect. Since this version of Link wrangles goats for his day job, he's already plenty strong, but he needs to anchor his feet properly to actually lift or pull heavy things.
Elemental-themed Warframes aren't immune to their own elements eg. an Ember can take fire damage, a Frost can have his shields reduced or be slowed by cold and a Volt can be electrocuted by a electrical trap.
In Saints Row IV The Boss gets super jumping early on, but also becomes immune to fall damage that would otherwise kill them in any previous game. When using their super speed they also gain the ability to knock cars, people, and other destructible objects out of their way.
An interesting aversion occurs in Hatoful Boyfriend with Anghel. At first it just seems that he's the resident Cloudcuckoolander, babbling away about ridiculous things, and acting as everything is taking place in a RPG game. Then you learn that Anghel secretes hallucenogenic spores, but doesn't have the Required Secondary Power of being immune to them, hence his strange behaviour.