Though there are multiple examples in Chrono Cross, the best by far is Miguel: a bespeckled, casually-dressed, mild-mannered man who looks like a librarian, and who will utterly hand you your own ass if you are not prepared.
Engineer: I appreciate that you're my employer, and an old man besides... but if you don't take your goddamn hands off me I will break you in half.
Really, the mercs (or at least most of them) fit this trope in general. They can be friendly, generous and even kind off-duty, especially around children and their respective loved ones, but in the field they are mentally unbalanced, bloodthirsty lunatics. Taken to the logical extreme with the Pyro.
Halo: Cortana is this, with Halo: The Fall of Reach in particular demonstrating that while she may be a nice if somewhat snarky AI, she will transfer you to the front line and ruin your marriage if you do anything to mess with her or John.
Sonic the Hedgehog: Cream the Rabbit, and her pet sidekick Cheese the Chao. She's amazingly polite, gentle, and nice to everyone. However, if you try to piss her off in anyway (particularly you, Dr. Eggman), she'll beat the living daylights out of you using her pet Chao. As if her Game-Breaker status in her debut title wasn't enough of a clue.
Try to kill Sonic when Tails is around. Just try it. He'll end your ass if you do, as Eggman found the hard way in Sonic Adventure 2
Sonic himself is generally an easy-going free spirit with no real ill will towards anyone. Cross anyone he cares about, however, and he'll plow through armies at Mach 3 to neutralize you, and that's when he's not even angry. Provoke him enough, and, provided he has the Chaos Emeralds around, he'll go Super Mode on your ass. Super Sonic is a Game-Breaker of epic proportions.
Janos Audron of Legacy of Kain. In Soul Reaver 2 he's a kind old mystic and the only person who's relatively straight with Raziel. In Defiance he's even more so, with a dash of woobieness when he starts to realize everything he's been enduring centuries of isolation for has been wrong... and then he's possessed by the Hylden and you get a peak at what a true badass he is.
The title character from Mega Man X. Having just watched Zero sacrifice himself against Vile, X regains all his health and proceeds to dispense an asswhooping on Vile and then Sigma.
Maybe because X wasn't really one of the titular "Nice Ones," just a Technical Pacifist, and has been beating up robot masters for quite a while before the scene you're referring to takes place.
His predecessor Rock, though. A childish, rather naive Robot Kid, Rock would be happy to while away his days as a lab assistant. When someone tries to use robots to attack people, though, he becomes Mega Man. He will plow through their forces, take their weapons to become a walking arsenal, and dismantle everything that stands between him and the threat. Lest you think Humongous Mecha will faze him, fuggedaboutit.
Especially in some of the later games, the original Mega Man nearly blows Wily away for good.
X in the Maverick Hunter X movie Day of Sigma definitely counts. Since it's set before the game, X was nothing more than a hesitant, unsure Hunter who took down criminals. Zero even remarks on how kind and sensitive X is. Then X scars Sigma's face with his bare hands after being stabbed in the gut.
Also, from the same game mentioned right above this entry, just right after you defeat Sigma's dog, X and Sigma will converse, and, oh my gosh, X was so angry, so angry, him shouting at Sigma alone can get you to crouch in a corner out of fear.
Justified due to the final fight against Vile and its result (see spoiler above) are moved to the 3rd Sigma stage, which means they just happened, and X is probably still emotionally wounded over it.
Let's not forget Iris from X4. Kill a girl's brother, and that sweet little British girl in a beret will come after you in a giant purple mecha suit.
A manga adaptation of X2 as X being so disgusted with the fallout of the first game's events that he put a seal on his arm cannon (he thought only his left arm could transform; that lack of knowledge had a hand in Zero's death). After his unit is killed by a traitorous subordinate, X finally undoes it and fireshisX-buster.
Patrick Sprigs from Mega Man Star Force generally acts mild mannered and sympathetic, yet secretly harbors hatred towards the parents who abandoned him, which violently manifests itself as his Split Personality Rey.
Which is justified by the nature of the thing in question, as well as the fact that most of the shady characters more-or-less worship Serenade, the cyber-side keeper of the Undernet server and implied to be Mamoru's Navi.
Onmyōji: This trope is in full play for Seimei and Yaobikuni near the end of the plotline. The former shows that yes, he can and does get angry, and the latter reveals that she's been putting on a nice facade all along in order to hide her Evil All Along nature.
Hibiki Takane of The Last Blade series is usually a kind, meek individual, who fights reluctantly. However, if the player keeps killing her opponents, she'll gain new win quotes and win poses included, and eventually a new ending that show her to have become a deranged murderer.
Vivi of Final Fantasy IX is sweet, innocent, kind, and despite his species, looks massively adorable, so naturally he has powerful black magic up the ying-yang. Most notably during the battle with Black Waltz 3 where the little guy just went ballistic.
Shown impressively at the beginning of the game when he's captured by a monster and then proceeds to fry the thing as it's sucking up his HP.
In Super Robot Wars Gaiden, Tytti Noorbuck is considered one of the more nicer, gentle-hearted pilot. Except at one occasion when she found out that Ricardo Silvera have attempted a prank on her 'little brother' Masaki. What happens next was her furiously choking Ricardo, while keeping a smiling face (good thing she's stopped early). Conversely, she completely drops the 'Nice one' persona when she faces her arch-enemy Lubikka Hakinnen, due to many reasons.
The Seraphim, and to a lesser extent, the Aeon Illuminate of Supreme Commander are more or less defined by this trope-they're normally devoted to nothing but peace, love, and hope. Force them into fighting, and they try to make the fight as short and painless as possible. In this case, "short and painless" involves genocide in the form of planetary-scale bombing runs, nuclear strikes, liberal usage of Humongous Mecha, and massive waves of land, air, and naval robots of increasing size and firepower.
This then becomes a Subverted Trope in the sequel, when it is revealed that the Aeon and Seraphim conversion methods include horrific brainwashing, an ancient conspiracy of political and religious saboteurs, and kidnapping. Then unraveled further when the Seraphim leader gloatingly reveals to his Aeon subordinate that he plans to nuke her as soon as his army emerges from the Quantum Realm.
Bastila is a relatively nice person most of the time, but she does happen to have enough Force power to change the course of any battle ever.
Several more are like this. Carth? Genuine Nice Guy. Pulls you out of an escape pod and nurses you back to health. Takes it upon himself to act as your voice of conscience. Mention Saul Karath and your will had better be made out.
Zaalbar? Painfully shy Gentle Giant and very honorable young Wookiee...who can still rip your arms out and beat you to death with them.
Mission? Very sweet-natured teenager, forgiving to the point where it can be a Fatal Flaw...and lived by herself in one of the worst Wretched Hives in the galaxy.
Revan. Even if redeemed and pursuing the Light Side path, it's remarkable how everyone seems to forget that Revan was the Dark Lord of the Sith and should not be underestimated. As shown by the storming of the Star Forge, even following the Light-Side will not stop Revan from mowing through an entire army and mopping the floor with their former Apprentice.
Safiya of Neverwinter Nights 2 is a very kind person most of the time. Until you threaten her mother or her golems.
Mass Effect: Good rule of thumb is if someone being nice, it's because they can afford to be nice.
The turians are generally pretty nice guys, are almost all unbelievably polite. They're heavily militarized, but strongly civic-minded, highly responsible, steadfastly loyal, place the greater good before the individual, and are quite willing to work with and protect other, weaker civilizations or species. And if you provoke them into war, they make damn sure you are never able or willing go to war with them again. Ever. They conquer everyone they fightnote Except for the humans, which has ever since been a major sore spot for them. But give you compensation afterward, just to make it perfectly clear how well this fits.
The Asari race are this in every way, shape, and form. They were the very first Council races, prefer peace and understanding above all else (The Asari Councillor in particular is less abrasive and more peaceful then the brash accusatory taurian or the constantly questioning Salarian). Asari matriarchs are considered THE most powerful individuals in the galaxy and asari biotics are considered the best of the best to such a point that a data file says they are nigh-unbeatable in one-on-one combat. Considering that after the first stage of their life-cycles they start seeking mates and then after that stage they start the stage of trying to find peaceful teaching positions (mind you this is the point where they're considered one of the most powerful individuals in the galaxy), as you find out first-hand during the first game, they can be terrifying.
Most of the Galaxy are quietly terrified of the human race for this very reason. From their perspective, humans are a Giant Space Flea from Nowhere that despite only having 7 years of Mass Effect technology under their belt, simply showed up one day and somehow managed to hold their own against the might of the Turian military for several months! Then after a ceasefire was quickly brokered by the Council, the humans simply declared the entire thing to be a good match and proceeded to enter the galactic community under a banner of peace!
Liara's level of niceness is over nine thousand, but her powers are such that she can telekinetically bench-press a Geth Colossus, and launch people practically into orbit by thinking at them hard. Even Wrex makes a point of noting how damn powerful she is. And if you attempt to hurt Shepard, she will dedicate every resource that she has to hunting you across the ends of the galaxy.
Kaidan Alenko is a relaxed, dorky type with absolutely no weapon skills available. But he can fire people into the sun with his mind and cause biological enemies to have toxic-flavoured seizures. He even ends his Training from Hell by snapping his turian instructor's neck with a biotic kick whilst defending another poor schmuck.
Tali is seen as being very polite and kind to most of her fellow crew members. If she runs across someone who she sees as evil, though, she can be... surprisingly vindictive. And amusingly creative; her reaction to a racist volus is to say that she knows intellectually that he's not worth getting worked up about, but emotionally she still wants to reprogram his suit's sensors to register the stench of garbage, all the time.
Commander Shepard him/herself can be the kindest, gentlest, supreme Paragon in the game. But even when played this way, s/he still gets a good share of ruthlessness, from threatening one of his/her crew with a gun to telling off news reporters who question him/her. S/he is also known for plowing through armies of geth, mercenaries, or Collectors and killing and pissing offReapers. For most of the first game, going pure Paragon makes it seem like Shepard simply cannot be angered, remaining polite and decent even in increasingly bizarre situations. Then the Overlord DLC from Mass Effect 2 rolls around, and the Paragon interrupt involves pistol-whipping a guy. Who completely deserved it.
In Mass Effect 2, Joker himself notes that Jacob is "way too nice a guy for all the ways he knows how to kill people."
Mordin Solus. Deadly Doctor. One of the most helpful of characters. Ex Special Tasks Group. One of the most ruthless party members. Easily butchered a few mercenaries that attempted to attack clinic. Hung their corpses out front as a warning to anyone else who would try.
One of Zaeed Massani's old war stories include being nearly strangled to death by a hanar, a jellyfish-like race whose racial hat is unceasing politeness and piety.
Kasumi is probably the most social and outwardly altruistic character in the second game, but if you piss her off she'll turn invisible and shoot you in the face or Parkour her way onto your ship.
Legion Is a "True Geth" Which means he does not mind organic life, he's actively polite, willing to answer what questions you have, still likes the Quarians despite the war, and will hold conversations with you about philosophy and such. Just be careful of whether or not your priorities endanger his race, he will blow your face off with a anti-material rifle, or hack his way through every bit of personal data you have.
The true Geth in general. Remember that during the Morning War, they were peaceful, subservient and just sat around contemplating the nature of their own existence. They only retaliated when the Quarian government began arresting and eventually killing pro-Geth protesters, although the nature of their retaliation was somewhat extreme. Oh, and if their help is secured in 3, they can potentially provide as many war assets as the Krogan.
The title character of Conker's Bad Fur Day was already having a bad day - as the title implies. All he wanted to do was to go home after a night of drinking, encountering Vampires, Zombies, bloodthirsty Dogfish, Cavemen, Dinosaurs, Robotic Haystacks, a horde of evil Tediz and a gigantic, opera-singing turd. And more. He's remained almost saintishly calm, up until the last level, where his girlfriend is brutally murdered by his boss, and her corpse thrown out into space by the xenomorph out of Alien, named Heinrich. He then proceeds to throw it into space, THRICE, before decapitating it with a katana, in one of the most satisfying ends to any boss fight ever.
The orcs from Orc Attack: Flatulent Rebellion were actually kindhearted beasts who lived in peace, until the humans showed up, polluted their land, and got all the orcs sick. They immediately went to arms and fought back against the humans as payback for ruining their ecosystem.
In a quest for Hunters, you have to kill four demons. The demons are in an alternate form. All of them are passive, and when spoken to, will respond cheerfully and positively, unless you are a Hunter. Three out of these four demons will use Fool's Plight on you if you even do as much as strike them.
In Cataclysm, there is the Shaman Erunak Stonespeaker within Vashj'ir. Very polite, saves your life a couple times, and doesn't seem very conducive to combat. Indeed, he doesn't get any combat...until the end quest. Then, he utterly OBLITERATES each force of Naga, one force with a MASSIVE Chain Lightning, and one commander simply by SLAMMING ITS FACE WITH HIS AXE. Believe me. You do NOT want to mess with this guy.
Cairne Bloodhoof, former chieftain of the Tauren. Very calm and peaceful guy. Kicked the ass of Warchief Garrosh Hellscream until treachery saw the end of his life. His son, Baine Bloodhoof, is basically the same way.
Generally speaking, any named character who's notably kind is anywhere from rather powerful to a Physical God. Most notable is Alexstrasza the Life Binder. Nicest dragon you'll ever meet who even forgave the orcs as a whole for enslaving her and her children during the Second War. Also the second most powerful dragon (after Deathwing) who will not hesitate to burn you to ash if she has to.
If Kingdom Hearts has shown one thing, it's that it's probably not a good idea to hack off Mickey Mouse...
To say nothing of the series' main character Sora. A happy-go-lucky kid who to date has defeated one thousand enemies in one fight, defeated most of the Disney villains at least once, and once cut a skyscraper in half and threw the pieces back at his opponent. (To be fair, the laws of physics weren't exactly in play during that last part, but still.)
We also learn that Goofy is capable of killing a man.
With only his shield at that, his character profile from the first game states that he flatly refuses to carry a sword or any other weapon of war, despite being Guard-Captain of the Royal Court Army in Disney Kingdom.
Yuna of Final Fantasy X. More in the sequel, but still in the original. To point: Yuna is captured by the Al Bhed. Tidus, Lulu, and Kimahri try to rescue her. After beating a boss, Yuna walks out of the hold on the boat she was imprisoned in, completely unharmed, and a guard slumps to the ground.
Lulu: I hope you hurt them.
Yuna: (modestly) A little.
Yuna is mostly the type who rather stays back in a fight and lets Auron, Khimari and Wakka or the Aeons handle the physical fighting. Though she keeps to casting healing and protective spells, you later learn why everyone is practically falling on their knees before her, and Badass Longcoat Auron and Kuudere Lulu allow her to run the show entirely as she sees fit.
Don't forget the sheer amount of damage Yuna's Aeons can cause. A fully charged Overdrive with the later Aeons can defeat most bosses single-handedly.
Early on she also can dish out more damage then the resident Black Mage Lulu if taught offensive spells.
And if you decide to take her down an offensive path on the Sphere Grid, she becomes a Lightning Bruiser that combines the offensive might and skills of someone like Auron with her own healing and defense spells. Lord help you if she decides to learn some black magic.
In BioShock you see the aftereffects of an object lesson in just how dangerous Little Sisters' Nigh-Invulnerability can make them if they're pushed far enough — in the area where they're converted, trained, and harvested, you find a corpse nailed to a wall with about a half-dozen of their giant syringes.
Also seen in the ending, where a bunch of Little Sisters swarm over the weakened Fontaine and keep stabbing him until he falls.
Leliana is a sweet, fluffy, girly girl who used to be a nun. She wants to show mercy to practically every sentient being you meet that isn't a soulless husk of pure rampaging evil, and the main character loses her approval every time s/he chooses an evil or selfish action. She's also a retired spy/assassin who's killed more people than she can even remember and can be leveled up into one of the single most devastating ranged attackers possible in the game.
Also, Sandal. A young and innocent Idiot Savant who can only say "Enchantment" in various inflectionsnote Or so it seemed until Dragon Age 2, which reveals that he can also say "Not" without his adoptive Father directing him, you stumble across him for the last time just before the fight with the Big Bad. He's alone, unarmed, covered in blood, and surrounded by heaps of Darkspawn corpses (including two Ogres). When asked what happened he of course responds with only a cheerful "Enchantment!"
Alistair is a goofy, friendly, optimistic guy who spends much of the game grieving for his dead friends and gets along with pretty much everyone but Morrigan. But if you want Loghain in your party in the endgame, do not appoint him the champion for the final duel at the Landsmeet, because this goofy, friendly, optimistic guy will casually decapitate his opponent in a spray of blood.
The Warden. Perhaps he/she is the most nice and friendly person in Thedas, but that doesn't stop her/him to kill everyone stupid enough to annoying him/her. One example is during Dragon Age: Origins – Awakening, when a group of Howe's former allies attempt a coup against The Warden. If The Warden took the Dark Wolf's way, such group of traitors suffers a lot of disappearances and deadly accidents until their leader's suicide.
Merrill is a sweet, innocent, Adorkable young woman with some trouble adjusting to human society and an awesome accent. She is also a powerful blood mage and has a strong mastery of various ways to zap people into a fine red mist.
Bethany as well. Sweet, cheerful, and well-liked by all the other party members (Varric nicknames her Sunshine), she is nevertheless quite capable of sucking in all enemies in a large area with magical vortex before engulfing them with ice and flames.
And Sandal deserves mention here as well, seeing as he takes out a roomful of Abominations and Demons, including a 'Pride Demon', right before the final battle, while still having the same CloudCuckooLander personality as before. Not to mention his creepy prophecy that comes out of nowhere...
Ah, Cole. Innocently Insensitive, sweet, physical-manifestation-of-mercy Cole. Who happens to wield a pair of daggers and is trained as an assassin so he can kill people as quickly and painlessly as possible. And don't you dare hurt innocent people or animals in front of him without a good reason.
Leliana again fills this role in no longer being a retired spy/assassin, nice if cold, and considered frightening by pretty much everyone. Perhaps the Inquisitor is the only one to cow her and only after jumping through a number of hoops, cares deeply for her friends and their cause, and jokes but seriously considers Murder Is the Best Solution to all the world's problems.
Wu Zi Mu of Grand Theft Auto: San Andreas, or "Woozie" to his friends, is a laid-back, friendly, unassuming Chinese man who enjoys playing video games, racing cars, and golf. He's also the boss of the Mountain Cloud Boys, a Triad sect - and when he finds his men wiped out and the Vietnamese gang responsible for it nearby, he rushes into the fray with a machine pistol and guns down everyone he can find, all the while shouting things like "Your blood will flow like wine!" - all this despite the fact that he's blind.
In Fire Emblem: Shadow Dragon, one of the few recruitable party units to attack you unprovoked is Wendell, the bishop who looks like the freaking pope. His dying quote mentions he has "no love for war", but you may remember that he's one of the only recruitable units who attacks unprovoked. Others include Roger, a hapless conscript who couldn't care less about war but doesn't have anything else going for him, and Jake, a gleeful ladies' man. Compare these with Darros the ruthless pirate and Navarre the stoic hired sword, who both try to talk to Marth or Caeda as soon as possible.
Occurs again in Path of Radiance and Radiant Dawn. Ilyana, a sweet weak thunder mage, will try and kill you if you don't recruit her first. Mia, a nice swordgirl, is also a pretty huge Blood Knight and can easily become the most competent sword-fighter excluding Ike. In Radiant Dawn, the main character is Micaiah, a nice, quiet light mage who can sacrifice her hitpoints to heal others. She's also the closest thing the Goddess of Chaos has for a human embodiment.
Played with in Fire Emblem: The Sacred Stones in regards to Cormag. His supports show that he's a really nice guy, but he's beyond enraged when he meets the heroes, because he thinks they killed his brother. Once he's recruited, Cormag returns to his Nice Guy original personality... but when he finds his brother's true killer, he breaks into an short but very scary speech about how he'll enjoy killing the culprit, borderline Evil Laugh included. And then, when it's said and done, he returns definitely to the gentle person he almost always is.
Many of the main character Lords count. They are for the most part noble, kind, self-sacrificing, peace-loving men and women who would otherwise never hurt a fly and would give anything for the happiness of others, but that doesn't stop them from commanding armies and mowing down enemies by the hundreds. And the gods help you if you mess with their companions or family. Some of the best examples of this include Lyndis, a kindhearted, understanding woman who never hesitates to help the two other leads and her support partners when they're going through tough times, who is also ruthless when it comes to bandits and pirates due to past trauma involving them, and especially after promotion becomes a speeding, double-hitting, constantly critting monster; and Marth, the 16-year-old, naive, sweet, somewhat childish prince who singlehandedly makes almost the entirety of the first gamea complete and utter joke, and while not overpowered, is a rather decent unit in later installments as well.
Also of note in the Lords is Roy, an unbelievably sweet boy who is about as much as a Nice Guy as his father (Eliwood, one of the stars of the prequel Blazing Blade), so kind he's one of the few lords who never says anything sarcastic or insults anyone, who while a very mediocre unit from the mid to late game, can become hilariously overpowered for the last few levels if one raises him right after obtaining the Binding Blade and promoting; in-story he is also one of the most accomplished lords, among other things being a Guile Hero and leading the entire united forces of Lycia to victory at the ripe old age of 15.
It's almost a general rule that the nicer and more unassuming a character is, the more likely you can point them in the general direction of the enemy army, alone, and have them win. From Fire Emblem Awakening's rooster, you have Sumia, a shy Pegasus knight with a gift when it comes to animals, and who gets access to devastating magic and one of the most broken skills in the game, Olivia, a dancer who can reclass into Pegasus Knight and also has a gift with animals, Donnel, mild mannered Farm Boy who always tries to make the rest of the company as happy as possible, possessing *the* best stat growth in the game, Stahl, average Cavalier who also tries to make people as happy as possible and wth very decent stats, Cynthia, Cute, but Cacophonic and naive pegasus knight (who gets access to devastating magic and the most broken skill in the game) obsessed with heroes ( And Sumia's Kid from the Future), and Nowi, a millenium old dragon who most of the times acts like a cheerful child...
A common trait amongst Pegasus Knights. Due to a combination of Speed and Luck that ends up being a complete Game-Breaker, they tend to kill everything in sight, but an unexpected number of Pegasus Knights in the series are Shrinking Violets. Some shining examples include the aforementioned Sumia, the sweet, naive, and innocent Tana from Sacred Stones, and the kind, supportive, motherly and peace-loving princess Caeda from Shadow Dragon and the Blade of Light, Mystery of the Emblem, and their remakes; the latter of whom is famous for being one of the most overpowered units in the franchise in Shadow Dragon's remake (albeit thanks to her exclusive weapon).
Tine/Teeny from Fire Emblem: Genealogy of the Holy War was at first a Shrinking Violet because she has had a very rough upbringing, what with being kidnapped since infancy and then witnessed her formerly plucky mother protecting her from abuses meant for her from her aunt and said mother dying in depression as a result and she was horribly abused ever since. Joining the liberation army thanks to her brother allows her to recover her psyche into a Silk Hiding Steel and a decently powerful unit... that has prepared some very venomous words reserved for those responsible for her abuses like her years-worth pent-up rage reaching boiling point.
Any good-aligned character in Fable games. In the second outing, and with enough experience, they will not hesitate to kick enemies in the face before chopping their head off with an enormous meat cleaver, knock them off of a cliff, shoot them in the crotch, knock their silly little attack aside and bash their heads in for their troubles, and all manner of other cruel applications of death and dismemberment. Probably while on their way to rescue slaves, collect on a bounty, or just give money to the church.
With the exception of Blue in Pokémon Red and Blue, every single Pokémon League Champion is perfectly friendly to the player in the field, then they clash for the title and pull out their team of Pokémon 15-20 levels higher than your own, all pumped up with the strongest moves they can know.
In Pokémon Gold and Silver, Gym Leader Jasmine is first seen literally having abandoned her post to take care of a sick Pokémon at the Olivine Lighthouse. She is also incredibly shy. Some more gameplay later, you get to fight her...and one of her Pokémon is a Steelix.
Also in Generation I, Red was a quiet boy who exemplified how important it is to care for Pokémon. After spending three years in Mt. Silver? Strongest trainer of the entire series.
In Emerald, Steven Stone is the equivalent of Red. Steven is generally friendly toward you throughout the story and even teams up with you to battle Team Magma in the Mossdeep Space Center. Once you beat the Champion, though, you can find Steven in the deepest chamber of Meteor Falls and battle him. His team consists of Skarmory, Claydol, Cradily, Armaldo, Aggron, and Metagross, and they are even more powerful than in Ruby and Sapphire as the Champion. The Prima Official Game Guide even says this:
He's friendly to you, but don't expect that friendliness to translate to the battlefield. He's merciless, and if you want to win, you must be, too.
Many Pokémon themselves also fit, like the sweet and innocent Togepi, who grows up into Togekiss who has the second-highest Special Attack of any Normal-type Pokémon. For a point of comparison, a Hyper Beam used by Togekiss is just as powerful as a Hyper Beam used by Arceus. And the Pokédex describes it as a harbinger of peace and goodness!
Cubone. Fridge Logic aside, there's a story of one that had its mother killed by Team Rocket. It picked up her skull and one of her bones and swore revenge. It doesn't help that back in the generation it was introduced, its evolved form could increase its Attack stat while attacking so much it would overflow. Did I mention it's a small, lonely Pokémon hiding inside an oversized skull?
Don't forget Dragonite. It's one of the most peaceful Pokémon in existence, until you realize its strongest move is called Outrage. You better not piss it off.
Same with Goodra. It is very cute and friendly and loves hugging it's trainer, but it's special defense allows it to take special attacks like they are nothing, and it's special attack and attack allow it to deal some serious damage back. It also learns Outrage too.
Drampa is a Gentle Giant Dragon Pokémon that likes to play with children. Threaten a child they've befriended, however, and you'll soon regret it.
Guildmaster Wigglytuff of Pokémon Mystery Dungeon: Explorers of Time and Explorers of Darkness is a fluffy pink rabbit who just wants to be everyone's friend. However, at one point in the game, he gets attacked from behind by three criminals he'd trusted. The outcome? All three of them are beaten to a pulp. This is mentioned as happening before when his team partner got knocked out by some bandits.
The partner character from Pokémon Super Mystery Dungeon is a Cheerful Child of the highest caliber and while they are content to simply explore the world to fulfill their dream of map making, they are more than willing to stand up for and rescue anyone in danger, including the school bullies. But then come the second half of the game that piles on various traumas onto them, followed by coming across one of Dark Matter's minions who turned their adoptive father into stone. They immediately beat him up almost to the point of unconsciousness.
James, the God of Earth in Sacrifice, is very down-to-earth, stressing pacifism or diplomacy for the first half of the game. Later, when it becomes obvious that warfare is the only option, he grants you a few useful tricks if you're his follower. Tricks like the power to make entire sections of the world fall into the abyss. If you wind up attacking his home in the Glebe, your introduction to this ability (Bore) will be when it eradicates most of the large army you start the level with. A double-edged sword as units lost this way take their precious souls with them, but it has its place.
Earthworm Jim brings us Peter Puppy. At first, he seems like a cute little puppy. But if you dare piss him off, he will turn monstrous and beat you up for massive damage.
And from the prequel we have not just an attack, but a character who plays this trope fairly straight: Sagi is an Adorably Precociouschild who is a major Momma's Boy and does pretty much everything to get money for her to run the orphanage back in his hometown. He even takes most of the villains' actions in stride and stays pretty upbeat and friendly while they're off wreaking havoc. Push him too far, however, and nothing will stop him.
Who's the killer in Heavy Rain? It's not the crazy junkyard worker and car thief, Mad Jack, it's not the crazy Rabid Cop Carter Blake, and it's not even the Psychopathic Manchild Gordi Krammer. It's frigging Scott Shelby.
The Liir from Sword of the Stars are mainly kind, understanding Actual Pacifists. Until you piss them off. We'd call in the survivors of the last race to piss off the Liir as witnesses to this, but none appear to be alive as the Liir wiped them off the face of the Galaxy (although they appear to be back come the sequel). In-game, the Liir start out extremely positively towards all races except the Zuul and are very easy to placate as long as you keep the peace with them — but if they first get annoyed enough at you to start a war, you'll never get them to back down again: They'll come at you until you or them are dead. Then the sequel rolls around, and we find out that the Suul'ka, the race that conquered the Liir and pushed them to this state of mind were their own crazed elders with powerful Psychic Powers. That's right, the Abusive Precursors that everyone lives in fear of are the Liir themselves.
The majority of Lux-Pain cast. Once they're infected with SILENT, you better look out.
MikeHaggar, Mayor of Metro City. Kidnap his daughter, and fear his pro-wrestling skills.
Dead or Alive: Kasumi is a sweet, kindhearted soul, and a Martial Pacifist through and through who makes it clear she dislikes even the thought of hurting others, much less killing. If you push her far enough or harm her loved ones and friends, though, you will know pain. Just ask Raidou, who, in the past, raped her mother, crippled her big brother Hayate and is an affront to everything she believes in and lives for. Oh wait, you can't: Kasumi killed him.
...only for Raidou to be revived as a cyborg by Donovan as of Last Round.
Super Smash Bros. Brawl showed that should the normally chivalrous but calm Link or Mario mistake you for severely harming their beloved Zelda/Peach, you will either get a sword or fist plowed into your skull. They're Nintendo's main examples of Good Is Not Soft for a VERY good reason.
Wendy in Rule of Rose. The sweetest girl you ever meet, but also a jealous Yandere. Also the protagonist Jennifer, herself. She may be meek and submissive and faint easily, but if you push her around long enough, she will push back with strength that terrifies the entire Aristocrat Club.
The title character of Klonoa. In the first game, he's a really nice, fun-loving Kid Hero. He even borders on Cloud Cuckoo Lander occasionally. Then his grandfather is killed.Joka did NOT survive the next level.
Wheatley from Portal 2. Normally he's a rather friendly yet dim-witted robot who tries to help you escape from the lab. That is, so long as you don't call him a moron. Do that, and all hellbreaks loose.
Garlot, protagonist of Blaze Union, is gentle and empathetic to a fault, and even though he has a short temper, he generally cools down very fast. He has self-confidence problems and spends a lot of his downtime wishing that everyone would just get along. And he's no pushover normally. But when bandit-by-any-other-name Pandra decides to sack Garlot's hometown, he goes into a state of cold rage so terrifying that every enemy in his path basically shits themselves in terror. In addition to this, inflicting serious harm on the people closest to him is a really, really bad idea.◊
Civilization: An Ascended Glitch turns Gandhi from very pacifistic to very militaristic when he invents Democracy. The game's Technology Tree means he can invent nuclear weapons soon afterward. If Gandhi threatens you with nukes, listen to what he has to say.
In Civilization V, Gandhi is the easiest leader to befriend. However, if you get on his bad side (be a warmonger, attack him personally), he will nuke your civilization into so much radioactive dust. Someone poked around the data for the game, and found a 1-10 scale on how likely a leader is to use nukes. The most warlike leaders (Montezuma and Alexander the Great) ranked about 8. Gandhi has a special rating of 12note scores above 10 get rounded down to 10 when the game starts, but there is a 2-step random factor for every score first to increase gameplay variation. Gandhi having 12 therefore means that while Montezuma or Alexander can be as nuke-happy as Gandhi, they can also be as low as 6, while AI Gandhi always is at 10.
The Psilons in Master of Orion are generally pacifistic and do not actively seek to conquer other empires. However, they have the best research abilities in the game, and will invariably be higher on the tech tree than you, which means they'll thrash you in a war.
Fallout: New Vegas has a few of these. On the Player's Team there is Veronica, a Brotherhood Scribe who wants them to play nice instead of raiding anyone with energy weapons but can also murder your face with a power fist, Arcade Gannon, a Follower of the Apocalypse doctor and researcher who wants everyone to be happy but is also a former member of the Enclave well trained in Energy Weaponry, and ED-E, an eyebot that just wants love and to find a home. Cass could also count, but she's an example of Good Is Not Nice.
There's also Christine Royce, a deeply philosophical Brotherhood of Steel Scribe who was Veronica's lover. When their former elder, Elijah broke them up, she joined the Knights and the Circle of Steel. When she heard about Elijah murdering people all over the wastes and abandoning the BOS at Helios One, she volunteered to hunt him down and assassinate him, becoming one of three people to explore the Big Empty and escape before assisting the Courier in killing Elijah and becoming treated as invulnerable as the security holograms to the Ghost People.
There's also Marcus and Mean Son of Bitch, two very friendly Super Mutants. Marcus, however, was a player companion in Fallout 2 and helped blow up the Enclave's Oil Rig and Mean S.O.B. defends Westside against the fiends so well that most of them stay away from Westside now.
Most of the low-level NCR troopers and Rangers can be seen as this. Most of them are nice gentle people, but they can kick your ass. Special note goes to Private O'Hanrahan, who doesn't want to kill people but in certain endings helps assisting his squad single handedly stop a Legion assault on NCR Ranger HQ at Camp Golf.
Similarly, Yes Man is an A.I. programmed to be helpful to whomever gives him orders and his default personality can be described as overly cheery. However, he's also the mastermind behind the plot to hijack Mr. House' plan to take over Vegas from both the NCR and Caesar's Legion. He's also the one who planned the attack on the Courier at Goodsprings. You can confront him about this, at which point he apologizes (not knowing who you are until you tell him).
As with Mass Effect, the player character, the Courier, can be one too, if you choose the "nice" paths. And then you can haul out your gatling laser and proceed to utterly destroy that group of raiders that thought you were easy pickings...
Likewise, Fallout 4 has a few examples, mostly on your side.
Curie is an unflinchingly polite and adorable medical robot with an accent and personality based on that of a woman Curie's creator dated at a university in Paris. However, as she'll tell you herself, "my offensive capabilities are quite formidable".
Dogmeat looks like an adorable wasteland mutt most of the time, but it's easy to forget he's still a very big dog with a lot of teeth, and will graphically rip people's throats out of sheer loyalty to you.
Preston Garvey is a total Officer and a Gentleman and the personification of the Minutemen's ideals, but he's also a Friendly Sniper who'll happily vaporise hostiles with his laser musket. To say nothing of the Minutemen themselves, as they're just ordinary wastelanders who have taken up arms to defend their settlements from various threats in the wastelands but will use heavy firepower to shell Raider and Super Mutant compounds into dust. If they're the faction the player leads to victory against the Institute, everyone is shocked that they actually pulled it off: even the Brotherhood of Steel are left nervous that the Minutemen had the firepower and balls to pull it off, and the the leader of the Railroad, Desdemona, will shoot you a smile and admit you really are a general.
Piper is a cute Intrepid Reporter who's just trying to uncover the truth behind things in the Commonwealth while taking care of her younger sister. Which in a place as dangerous as the Commonwealth means that she's really good with a gun.
Avion from Shadow of the Colossus is generally considered the second most peaceful colossus in the game, by virtue of the fact that it will never attack Wander until provoked. Until Wander makes an attempt to harm it, Avion is content to sit on its perch and watch him swim around the lake... but the second Wander shoots an arrow at it, Avion will come swooping down to divebomb him. This attack is a one hit kill in Hard mode if Wander is not successful at dodging it, and is pretty damn scary otherwise.
Super Mario Bros.: Luigi is generally a pretty nice guy. If you threaten to harm Mario, he becomes an unstoppable force. To whit, in Mario & Luigi: Dream Team, when Mario looks to be in extreme danger in the Dream World, Dreamy Luigi grows giant and in one case, slams backwards a sentient volcano only with his hammer! Even more impressive, Dreamy Luigi is able to hold his own against Giant Giant Bowser. As in, Giant Bowser made even more giant to the point where Giant Luigi barely comes up to his knee. The last Giant Battle is activated not by fear but by sheer willpower as well.
Luigi: Nobody messes with my bro!
Don't mock his mustache either. This was was actually very plot important: It was part of the Batman Gambit in Dimentio's Xanatos Gambit to get Luigi brainwashed and take over the worlds. He succeeded in brainwashing Luigi, but after... well, Dimentio became the only villain in the game to get a Game Over.
Before that, in Paper Mario: The Thousand-Year Door: The Happy Lucky Lottery is run by a nice, happy, optimistic Bob-Omb named Lucky. You get a new chance to win in one real time day, determined by the Gamecube/Wii clock. Unlike other games where you can abuse the clock if it affects the game... Lucky will go berserk if you do so. Do it twice and you get a Game Over.
Noel Vermillion's hobbies include shopping via the internet and writing poems. She likes cute things, and dislikes bugs, especially ones with lots of legs. That said, if you mock her chest size or her intellect, Bolverk will perforate your skull. Then there's also the fact that she can transform into Mu-12, which is her Super Mode and is dubbed as Kusanagi, the sword that slays gods.
Makoto Nanaya is a silly, friendly, generally whimsical and energetic person, and also appears to be somewhat scatter-brained. However, she makes it clear to Tager, "If, for whatever reason. Noel Vermillion is harmed in any way, I will hunt down that person and make them pay... dearly." This is neither hyperbole nor limited to Noel - attack any of her friends and, unless you're one of them (hi, Carl), you are in for a world of pain. Let's not forget that her Astral Heat involves punching the opponent so hard it shatters the moon.
Dark Dawn introduces Sveta Czamaral, a shy, sweet, troubled girl from the kingdom of Morgal. Who can turn into a seven-foot-tall werewolf with an attack rating that makes most of the game's bosses blush.
In Diablo III, the Hand of the Prophet are a group of girls who served under a powerful Vizjerei lord prior to encountering the aforementioned Prophet. Eirena, one of them, is quite friendly throughout the nephalem's campaign, and yet she was thirteen at the time she and her sisters murdered their lord, his buddies, and the greater daemon the Vizjerei were summoning.
Tales of the Abyss: Fon Master Ion is polite and friendly to a fault (and is rather feminine looking), but he wields some of the most powerful fonic artes in existence. Not only that, he's also one of the most powerful people in the world politically, and knows how to use that power effectively when push comes to shove...like the time when he threatened to stop reading the Score (the giant prophecy that everyone relies on to determine what they should do, often on a daily basis) for an entire country if any of his companions are harmed.
Eleanor Hume is a sweet and gentle girl with Incorruptible Pure Pureness who joined the exorcists to help people and (before she joins the party) is distracted from chasing Velvet several times because she's doing random odd jobs for civilians. Once she joins the party, she spends most of her time patching up everyone's clothes and trying to get them to help bystanders. However, when she meets the demon who killed her mother, she goes absolutely berserk, flying into a blind rage and nearly turning into a demon herself.
Eleanor: I hate you I hate you I HATE YOU!
Velvet herself, though we only see her "nice" state a few times, such as at the beginning of the game. She was a friendly girl living with her brother-in-law and working to provide for her sick little brother until she witnessed her brother-in-law murder her brother, and the rage turned her into a demon. In fact, she's nearly identical to Eleanor, except she's been stuck in a berserk rage for years.
Velvet: Why did you kill him?! His blood... on your hands... Answer me! Answer me! WHY?! He was my brother! My Laphi! What did he ever do?! GET OUT OF MY WAY!
And come Hyperdimension Neptunia Victory, Plutia blows them all out of the water. Normally lazy, friendly and scatterbrained with just the vaguest hint of a slight sadist streak, major villains are known to rethink a confrontation if it means she might transform. Why? Because Iris Heart won't kill you. MadamGoddess will make you beg for permission to die.
Plutia is the most extreme; though Peashy gets this too. Even before she was transformed into Yellow Heart she routinely beat the crap out of people and she's cute as a button.
All the CP Us fit this in Megadimension as they've reached a point where they love their people and friends and come off as kind; but threaten those close to them or their countries and they will end you.
In a similar vein to Dr Mordin Solus in Mass Effect, Dr Lokin in Star Wars: The Old Republic is a talkative, polite old man. One might mistake him for a bit of a dork even, but under the facade he's a ruthless man who survived this long because he knows the tricks of the trade, and mind you, his trade is Imperial Intelligence. note When your party is being tortured, he mocks the torturer saying he's "done worse to family." And then there's his fondness for rakghouls...
And then there's Lord Zash, the nicest and most polite Sith you will ever meet. Khem Val notes that she "reeks of death". It's all an act, but a pretty good act
Likewise, a Light-side Sith player character is regarded as an oddity by non-Sith, while your fellow Sith (especially once you start climbing the ranks at breakneck speed) regard you as far beyond dangerous because they don't know the true limits of your power behind your facade of kindness and humility. It's lampshaded by Darth Ravage at the end of the Sith Inquisitor storyline, if you choose to thank them for granting you a seat on the Dark Council.
Louis of Left 4 Dead is the most optimistic of the survivors and generally keeps a positive attitude (which drives Francis nuts). However in the Death Toll campaign when the Church Guy refuses to open the safe room for them, Louis threatens to beat the crap out of him with his gun.
Louis: "Mister, if one of us gets killed out here, I will shoot my way in there and beat you to death with my gun!
All the yordles (minus Veigar, who is megalomaniac; and Rumble, who is basically an egotisitcal mad scientist) from League of Legends can easily fall into this trope. More particularly true with Teemo, who spent most of his time in isolation through his scouting missions and he's slowly show signs of his mentality being cracked apart. Luckily, he's good friends with Tristana and has her in company.
Nightwolf from Mortal Kombat, especially when he gets more characterization in Mortal Kombat 9. Polite, properly reverent towards actual gods, contemplative, insightful, patient, and doesn't so much as drop a sarcastic line, even towards other characters who sorely deserve one. He also won't hesitate to inflict a brutal beatdown to foes or give his life to save others if necessary.
The Salt Hogs from Startopia are a race of salt-of-the-earth, porcine aliens with a hardy Protestant work ethic. As well as working your recycling plants and factories, they also all come armed. They get along with most other races very well (except for those nasty, snobbyPolvakian Gem Slugs) and while they don't fight as well as Kasvagorians, they do happen to be a lotcheaper to hireen masse. Their cultural version of Christmas apparently involves handing out a random selection of various non-lethal toxins to their kids alongside the more traditional gifts, to teach them that life isn't fair and they need to take the rough with the nice.
Rick Taylor, protagonist of Splatterhouse, was just a Hollywood Nerd with a good relationship with his girlfriend, Jennifer. Unexpectedly, in each game something comes to take her from him, leaving Rick to don the sentient Terror Mask to save her and leave everywhere in his wake splattered with blood. In the remake, the Terror Mask invokes this trope by telling him that he loves killing the demons as much as it does. While Rick at first denies this and is disgusted with the Mask's brutality, later on he doesn't deny it in the slightest. And judging by his Finishing Moves, he is not a Gentle Giant you would ever want to mess with.
Humans are this in the backstory to Galactic Civilizations. Just as the Xendar... Oh wait, you can't. Why? Because they're all dead. Apparently, not long after humanity stupidly gave the hyperdrive secret to the other races, the Drengin decided to get rid of humanity, whom they perceived to be a race of diplomats. Instead of attacking humanity directly, they found a warlike pre-spaceflight race called the Xendar. Quickly upgrading their tech to the galactic level, they unleashed them on humanity, expecting humans to try to talk their way out of it in vain. Instead, the Terran Alliance cranked up the military-industrial complex and beat the Xendar so hard, there are none left. After this, the humans put away their weapons and start talking peace again. The Drengin treat this event as evidence that humans are liars, talking peace while secretly planning for war.
Ying from Paladins is always putting her friends first in her dialogue and is one of the healers, but if you're not careful, she can take you out just as quickly as any of the other heroes can.
Undertale has many examples, what with its tagline of 'Friendly RPG'. That said, one example stands above the rest: Sans the Skeleton. They may be chill and friendly, if a bit childish, but one glance and you can tell there's more to them than meets the eye. If you want to find out just how deep, go for the No Mercy route, but remember: You're gonna have a BAD time.
Eskel in The Witcher, in particular in the third installment. Eskel is a genuinely Nice Guy, calm, affable and unfailingly courteous. He is also quite capable of matching Geralt, known as the finest swordsman in the world, in a one-on-one duel, and is slightly better than Geralt at magic. He also manages to duel Caranthir, an eight-foot tall, fully armored, millenia old, staff-wielding teleporting sorcerer (Squishy Wizard is definitely NOT in effect) to a stand-still.
Nanashi, the player character of Shin Megami Tensei IV: Apocalypse can be this if the player chooses the good aligned dialogue choices. He's a kind, supportive ally who helps his friends in their time of need. He's also an unstoppable undead Godslayer who cuts a huge swath out of at least two armies and kills their respective leaders in less than two weeks. If the player picks the Massacre route, Nanashi moves into Affably Evil territory. Beware, for the Nice Guy can also be an Omnicidal Maniac...