The shadow warriors of medieval Japan, reputedly possessed of all manner of mysterious powers known as ninjutsu, including invisibility and intangibility. Able to infiltrate even the most heavily guarded fortress without being detected. If they are caught, they may trick their pursuers by mysteriously swapping places with a log. They may be portrayed as cutting down any opposition superhumanly swiftly. Traditionally dressed in black bodysuits with black masks or veils to hide their faces (or sometimes in white). They are the ultimate spies and assassins, gifted with their own deadly magic and martial arts. Born in hidden villages, they are trained from birth to obey nindo, an alternative code of honor to bushido; to show no pain, feel no emotion, and remain loyal to their clans under pain of death - or the third code of getting as much money as possible.
Or so popular legend has it. While ninjas did indeed exist, their reputation for invisibility and infiltration more likely stemmed from their willingness to dress as members of a lower social class when no one else in Japan would consider doing such a thing. Their "invisibility" was part psychological in cause — by dressing as a peasant, they were ignored and dismissed, or never even noticed at all, by the upper classes, a useful thing despite the oft fierce travel restrictions on the lower classes. Superior knowledge of survival skills, a lot of actual stealth, poisons, assassination techniques and unorthodox tactics (added to the fact that the ninjas actively encouraged the spread of rumors of their magical abilities) were the most important though. A popular myth states that ninjas came from lower classes (at least compared to the samurai) and they were often hired to do the dirty deeds honorable samurai would not do, but in reality ninjas were usually samurai, or in some rare cases, mercenaries who work for samurai. Ninjas were mainly used for espionage and sabotage, and sometimes assassination.
Ninjas were also quite skilled with a variety of tools, such as the multipurpose kunai knife trowel. Plainly put, while a stereotypical ninja would jump around on rooftops in ridiculous clothing, a real ninja most likely would simply infiltrate the household staff and poison a meal. Among many other things, a good ninja always knew where hissanjaku tenuguiwas.
The "classic" black ninja costume is, in fact, the outfit worn by stagehands in traditional Japanese theatre. Japanese stagehands are frequently in full view on the stage, but the audience was trained to ignore them and thus are considered "invisible" by the audience. It became the practice to hide ninja characters in full sight by putting them in the same outfits as the stagehands, for a startling effect when characters were suddenly attacked by "thin air". The stereotypical black "ninja outfit" is actually horribly conspicuous, even at night. For night stealth, real ninjas wore dark blue outfits; someone dressed in solid black will stand out like a silhouette. Usually, though, ninjas simply dressed like ordinary people (peasants, monks, merchants, scholars, etc). That way, they can move about unnoticed, day or night.
Female ninja are often called kunoichi in a pun on the Japanese kanji for woman (女, onna/jo), which looks like it's made up of ku (く), no (ノ), and ichi (一). Kunoichi are often portrayed in media as experts in seduction and poisons. Or both at the same time. Kunoichi are also often seen in outfits that combine a hodgepodge of traditional clothing, fishnet, bared skin, and strategically-placed weapons.
In some works of fiction, ninja are divided into three ranks: genin (lower), chūnin (middle), jōnin (upper).
Legendary ninja include Fuuma Kotaro, Hattori Hanzo and Sarutobi Sasuke. While commonly thought to have originated in Japan, ninjas may have originated in China, and the idea and practice later spread to Japan. Historically, the word "ninja" was not generally used; in Japanese historical documents, shinobi was often used.
In American movies, especially the ones from the '80s with "ninja" in the titles, only the hero ninja and the Big Bad ninja make any pretense of stealth or invisibility — and sometimes, not even them. Any underling ninjas will be the class of mooks known as Highly-Visible Ninja. In the late 20th Century, they becamethe arch-enemies ofPirates, for no reason other than theRule of Cool.
One of the earliest Japanese cultural tropes to make it to the West, where it has now branched out into the McNinja franchise. Look for ninja to make use of the Smoke Out, the Flash Step, the Fuuma Shuriken and the aforementioned Ninja Log.
Compare The Hashshashin, the Middle-Eastern counterpart.
Sub Tropes include:
Samurai Deeper Kyo has many ninjas on both Kyo's and the Mibu clan's side. Sanada Yukimura has the Jyuuyuushi (The Ten Sanada Brave) which includes Sarutobi Sasuke and Kirigakure Saizo. Fuuma Kotaro is Sasuke's childhood friend, who is also one of the Jyuunishinnsho (The Twelve Heavenly Gods) and believes Sasuke had betrayed him.
'Ninja' in this series seems to simply refer to those who use ninjustu skills. The ANBU black ops division would be the local equivalent to ninja, as a group of elite warriors who are assassination experts.
The OVA version of Sakura Taisen slyly acknowledges the origin of the traditional ninja garb— The stage crew of the Imperial Theatre — the secret headquarters of the Flower Division — are all ninja, and ninja with all manner of "ninja magic" at that.
The Canon Foreigner Sasuke Sarugakure in Ranma ˝ subverts the character type by being borderline incompetent (he's clumsy and has virtually no combat capabilities, but is a master of stealth and can move too fast to be seen) in a neighborhood filled with world-class non-ninja martial artists. In the manga, Wholesome Crossdresser Konatsu plays it a little more straight. Ukyo Kuonji uses a spoof style that merges archetypical ninja moves with cooking tools.
Similarly, the ninja in Ninin Ga Shinobuden are incompetent ninja who usually don't even carry shuriken; when they all suddenly produce shuriken and every one hits its target, causing another character to think that maybe they are skilled after all, one calls his mother on a cell phone to tell her that he has touched a shuriken for the first time.
Almost assuredly parodied in G Gundam. Midway through the story a German ninja is introduced and takes on the role of surrogate mentor to the protagonist, Domon. He even practices German Ninjutsu. Hilariously enough, he shuns the traditional garb of a ninja and dresses in clothes that are not remotely useful in maintaining stealth. Most absurd is the mask he wears. While it does obscure his features, it is painted in the bright, primary colors of the German flag and sports a jester hat-like protrusion.
While he looks ridiculous, Schwartz is otherwise a straight example of a ninja. He's also extremely Badass, able to fight on roughly the same level as Master Asia.
Himawari!! and its sequel series are all about the ninja. Most of the ninja in the series actually are fairly stealthy. The heroine herself...not so much.
From the Red Ribbon arc from Dragon Ball we have Purple (what title he has depends on whether your watching the original or the dubbed version). He doesn't have any true powers, but he pulls a lot of classic ninja tricks including doppelgangers (Cardboard) invisibility (hiding under water with a straw to breathe) ... er ... he's not very good at it, okay?
Akira from Mai Hi ME and Mai-Otome uses a lot of classic ninja tricks and tools, including shuriken, kunai and smoke bombs. She also uses the title "Secret Ninja", while fighting in disguise (which doesn't fool anybody). Curiously, sometimes she's seen interacting with other shadowy kuroko-wearers, implying that she indeed is a genuine ninja from a genuine ninja clan, even though that never becomes a major plot-point.
Bleach: The Onmitsukido is an entire organization of ninja comprised of several families who serve the Shihouin Clan. Yoruichi was the 22nd head of her family and the first woman in its history to become head of the Keigun (lit. "Punishment Squad"). When she and her friend, Kisuke Urahara, defected from Soul Society, she was succeeded by her protege, Sui-Feng, as both head of the Keigun and as captain of the Gotei's 2nd division. Making her the first member in the Feng Clan's history to ever attain a position of power; in addition to being the second woman to ever hold both titles.
Variable Geo: Chiho Masuda is a ninja waitress, in service to a shadow organization that has secretly monitored the events of the VG tournament since its inception. She enters the competition under orders to investigate The Jahana Group's activtities in order to find evidence of their corruption and expose them.
Ryuusei no Rockman (AKA Mega Man Star Force) has an entire episode devoted to Ninja. Highly-Visible Ninja with all the typical tricks. Though, the guy teaching the main cast the tricks of the trade is damn good at it. They add -de osaru on the end of every one of their sentences...and apparently, the art of ninjitsu was developed by people from the ancient civilization of Mu. One of the Ooparts is a Shuriken, and Mega Man can take on the form of a ninja... Of wood.
The manga Hanzo no Mon (titled Path of the Assassin in the Dark Horse translation) subverts the stereotypes regarding ninja attire; although Hanzo (and his wife) are ninja (usually called suppa), they wear light armor on the battlefield and the stereotypical ninja outfits when they need not to be seen at all, but otherwise wear context-appropriate clothing and act accordingly. Likewise, certain ninja have notoriety and may even appear openly when a lord holds court. In fact, Hanzo, his wife and Hanzo's ninja relatives have their wedding ceremony in normal noble/samurai clothing! (After she demonstrates her abilities as a ninja wearing "the" outfit.)
Kirino and her village from Ai Kora. Kirino herself doesn't exactly /hide/ the fact she's a ninja, but she doesn't announce it to the world, either. She's another subversion of the ninja attire stereotypes, in that she wears ninja clothes in her village, and context-appropriate clothes everywhere else.
The two main families of the anime Basilisk are all very competent ninja with unique skills that range from cool to plain freaky. Its story is often summarized as "Romeo and Juliet, with ninjas".
Sonic X has Espio the Chameleon. He is (unlike the others in his group) calm and collected. As a part of the Chaotix detective agency, he made his debut in episode 39 (a loose tie-in with the game Sonic Heroes). That was, however, his only appearance on Earth. In fact, that was his ONLY appearance in the original 52 episodes! He would later go on to appear in episode 59, where he is again seen with the Chaotix crew. During season 3 he became more of a prominent character. The appearances of the Chaotix were strictly for filler episodes until episode 74, where they became background characters for each of the remaining episodes, participating in combat against the Metarex. Akin to his video game counterpart, Espio uses all manner of Ninja skills to battle opponents. His trademark ability is to turn invisible to sneak up on his enemies. He also uses a variety of weapons including an enormous collection of shuriken, and even threatens Sonic's life at one point with one of his kunai ninja knives. Despite his limited appearance in the series, he is somewhat of a fan favorite.
Change 123, in its later volumes, introduces an all-female ninja clan whose members infiltrate into Motoko's school to recruit Motoko (or, rather, to recruit her alternate badass personalities). Unlike typical Highly Visible Ninjas, they actually blend into the normal world, wear plain clothes (even when they're in their ninja village), and use weapons which are disguised as normal everyday objects. Also, the words "ninja" and "shinobi" are mostly avoided. Instead, they talk about "our clan/family", "our business", "family business" and similar.
Like their game counterparts, Koga and his daughter Janine in Pokémon Special are modeled after stereotypical ninja, but the author obviously had some fun making their techniques even more ninja-esque, such as outfitting their Pokeballs into shuriken. At one point, Janine even uses hand seals, presumably as signals to command her Grimer without having to actually say anything out loud.
There's also a trainer class in some of the games, whose methods involve hiding and then springing out to battle whomever passes by.
Furthermore, the moves "Double Team" and "Substitute" are based on popular ideas of ninja techniques.
One two-part episode of Speed Racer featured ninjas who drove ninja racecars. Since American audiences at the time had not yet heard of ninja, the dub for American TV called them "assassins."
Soul Eater's Black Star and Tsubaki. Black☆Star is your typical Highly Visible variety, and somehow manages to make a big deal of being 'stealthy' even when he bothers to try. Tsubaki is a member of a clan of ninja-associated Living Weapons (kunai, (big) shuriken, smoke-bomb, camouflage, katana, chain-scythe) and frequently has to remind her meister how he should be behaving. Such as the fact that telling your target you're here to assassinate them is a bad idea.
Digimon has a number of ninja-inspired monsters. Two notable examples are Ninjamon and Kougamon, his Pallete Swap. It should be noted, in Japan, he and Kougamon both take their names from regions and styles associated strong with the ninja arts. Other examples include:
Falcomon, who's a rather straight example of this trope, along with his evolutionary stages. His Champion form, Peckmon, is a Ninja Ostrich.
Gintama is another example of the Highly-Visible Ninja variety. It has Ayame Sarutobi using her ninja skills for stalking of all things.
There's also Zenzo Hattori, The Oniwabanshuu and the Shinobi 5.
Ninku: The heroes are all Ninjas who face off against some former Ninja as well as practitioners of other ethereal martial arts such as Feng Shui users. The Ninku gain their powers by drawing on the power of the elements themselves which take the form of a dragon. This means they aren't constrained to chi or chakra or some finite internal reserves.
One of the antagonists in Katanagatari is the Maniwa Corps, which is filled with ninja that rival Naruto in the visibility department.
Nabari No Ou takes place in a ninja world called Nabari which are full of modern day ninja.
Rurouni Kenshin has the Oniwabanshu, a clan of Kyoto-based onmitsu that are initially opponents to Kenshin under the leadership of Shinomori Aoshi. When Kenshin travels to Kyoto to fight Shishio Makoto, they become allies.
Brave 10 is a fantasty manga and now anime series drawn by Kairi Shimotsuki which centers around the Ten Braves of Sanada Yukimura. The tagline for the series is 'stylish ninja action' and boy there a lot of ninjas.
Ninja are one of the major types of opponents faced by Ogami Itto of Lone Wolf and Cub. They're depicted very realistically, between the Kurokuwa ninja, spies and assassins of the shogunate, and the "Grass" ninja, who functions as extreme deep-cover agents and spies. Masters of disguise and employing all manner of "dirty" tricks imaginable, ranging from poison to psychological warfare, ninja provide Ogami's greatest challenges in the first half of the series. By the finale, after the Kurokuwa have all been lost in failed assassination attempts on Ogami, Retsudo calls in the Grass for one last desperate attempt. When all is said and done, Ogami has managed to kill his way through every ninja in Japan.
Nobuo Matsuri of Ninja Papa is a retired ninja. Or he would be if he weren't forced to bust out his deadly skills at least once a chapter.
Senran Kagura is a videogames series where sexy ninja-in-training schoolgirls from different schools fight each others, and is some strange blend of comedy and drama : in spite of being heavy on the fanservice side (the series is marketed as cute & sexy hyper-breasted battle action), the characters are deadly serious about their ninja duty, some of the backstories are quite dark and the worldview is rather truthful to the hard-boiled world one would expect from a ninja world.
Shura Kirigakure from Blue Exorcist is the descendant of an ancient clan of female ninjas.
It has been a common character type in American comics since the 1980s; for instance, the Marvel Universe villain clan, The Hand, cropped up then, and during that period, Frank Miller effectively changed Daredevil into one. Many, however, have noted that creators of Batman created him as a de facto ninja character without knowing it in the 1930s.
Miller also wrote a ninja into Sin City in the form of deadly little Miho, the primary enforcer of the girls of Old Town. She is the single deadliest Dark Action Girl of the series, the only one of the girls of Old Town who does not use guns, and a heroic example of the Psycho for Hire.
Dwight: Deadly little Miho. She'll cut you quick, she'll kill you quiet. You won't feel a thing, not unless she wants you to.
Snake-Eyes and Storm Shadow (among many others, some of whom we do not speak about) from G.I. Joe. The unnamed "narrator" of the Order of Battle series and the action figures File Cards (actually Card and comic series writer Larry Hama, writing in-universe observations about the characters) said "The great Ninja assassin clans disappeared a hundred years ago. If they were wiped out, nobody took the credit for it and if they're still around, who are they working for?"
Molly: Does being a ninja count as having powers? Victor: It counts double!
Often appear in the works of Adam Warren. Livewires has Hollowpoint Ninja, Empowered has Ninjette and several clans of ninja.
Usagi Yojimbo, being set in feudal Japan, frequently features ninja. They range from enemies to allies of Usagi, with three main clans present: the Neko clan which is feline, the Mogura clan which is comprised of anthropomorphic moles and the Komori clan, which features razor-winged bats.
"When you fight as many ninjas as I have, you can't help learning some of their tricks"- Wolverine; "Get Mystique"
The popularity of ninja in Western media may have started with the James Bond film You Only Live Twice from 1967. Most of those ninja were depicted as being more like members of an elite government special forces unit than invisible assassins, however. (Except for the one who killed the Bond girl, of course.)
In Licence to Kill it is revealed that Hong Kong Narcotics employs ninjas as special agents. (Given that the Special Duties Unit of the Hong Kong Police Force were trained by the SAS before the colony was handed back to China, this may not be as far fetched as it first seems.)
Appear in The Last Samurai, with some of their methodology were accurately presented.
The Shaw Brothers kung fu movie Heroes of the East features a ninja. Early in the film, the Japanese wife (Yuko Mizuno) of the kung fu hero (played by Gordon Liu) gives him a demonstration of ninjutsu. He is not impressed. Later, the hero fights the wife's old boyfriend, an actual ninja (Yasuaki Kurata) and out-tricks him at his own game. In both cases, the ninjutsu is based more on movies (Japanese ones rather than American ones): sneak attacks, hokey peasant disguises, gunpowder, etc., but does involve some real weapons. Even the costume is based on Japanese theater. The film subverts several ninja conventions: one, the ninja is portrayed as a man of skill and honor; two, the ninja is not out to kill anyone; three, his allegiance lies with his martial arts teacher, not a feudal lord.
Hong Kong filmmaker Godfrey Ho produced about 50 ninja movies in the course of less than ten years. His style was to cut and paste using stock ninja fight-scene footage edited into unreleased Hong Kong films, many of which had nothing to do with martial arts. Ho also employed unemployed Caucasian actors, typically as villains, Vice cops, or Interpol agents. Veteran actor Richard Harrison played the role of heroic ninja master Gordon in a number of these films, although Gordon's role and backstory varied with films. Due to the cut and paste nature of these movies, it appeared that there were two different stories going on at the same time. It was easy to differentiate the fairly recent "ninja" footage from the grainy "old HK film". The two protagonists often appeared to interact with each other through clever editing or phone conversations. Godfrey Ho Ninja Movies were also known for the tacky ninja outfits that ranged from red, to yellow, and even metallic colors. Ninja frequently wore headbands with the word "Nin-Ja" embroidered on them. The word ninja was regularly pronounced "ninjer" in many of these films due to the accent of the English language voice actors.
The unidentified assassin of Pharaoh Amenemhat I from Papyrus Millingen is the Ur Example of ninja. Yes, the first ninja in historynote Currently, at any rate; who knows if there is any older literature who features them. is an Egyptian.
Ninjas in Cloud of Sparrows are rather more plausible than most other examples. They are very stealthy and good at dodging pursuit, but dress in normal clothes and are primarily employed as stealthy assassins and spies. Kudo, one of the two main ninjas in the book, also indulges in a spot of Clark Kenting. He is also revealed to have poorer reflexes than gunslinger Matthew Stark.
The antagonists in The Gone-Away World by Nick Harkaway are a ninja clan turned corporate empire.
Phoenix Force battled the Tigers of Justice, a radical Japanese group using ninja techniques to attack nuclear power plants to avenge Hiroshima and Nagasaki. In later books they receive the help of John Trent, a Japanese-American master of ninjutsu.
The pulp magazine version of The Shadow was essentially a ninja...with guns and the coolness factor turned Up to Eleven.
Lady Catherine de Bourgh has ninja guards in Pride and Prejudice and Zombies, and can't see the logic of anyone not having them. Elizabeth, however, makes short work of them, even taking out a heart and eating it.
Timothy Zahn's Blackcollar: The Blackcollar commandos are obvious ninjas IN SPACE!. Their favored weapons are shuriken and nunchaku — low-tech to avoid enemy sensors.
In the Discworld novel Thief of Time, the Monastary of Wen the Eternally Surprised has stereotyped ninja as Time Police. Lu-Tze is highly contemptious of running around rooftops in black outfits ("others trained them, I just tried to undo the damage"), and his own strategy of passing unnoticed as a humble sweeper is closer to the real ninja.
Similarly, Pratchett had to be thinking of this in "Interesting Times", after making fun of the Highly Visible Ninjas in Wutai in an earlier chapter, Rincewind discovers that by wearing a farmers hat; nobody looks at him.
but averted by Vetinari, who wears green and grey as a student; and subverted in that quite a few Assassins never actually "inhume" anyone, preferring to use their conspicuous black clothing to attract women, use their obvious presence to act as a political lever, r various other uses.
They appear in Taiko, but realistically, as common spies who are looked down upon by samurai.
The title character of the Alex Rider series dresses as a ninja in Scorpia, when going to assassinate Mrs Jones. However, he does use real ninja tactics when trying to gain access to her floor: disguising himself as a pizza boy and having his weapons hidden in or disguised as his merchandise, and only switches to the stagehand outfit when in an area he'd be thrown out of whatever he was dressed as.
In lonelygirl15, Bree describes Tachyon as a ninja in "Training Hard". Ninja are also parodied in "My School Project" and the remix version, "Ninja Video by ElizKM86", during which Danielbeast makes a movie about ninja.
As are the Assassins of the Dark Elves. Their leader, Shadowblade, is so awesome he can disguise himself as a mook of the enemy army. Even if they are composed of magically-reanimated corpses. Did we mention his skill with weapons is so great he can match an incarnation of the God of Slaughter in terms of sheer skill, and outmatch it in speed?
A certain fan-made army book for Nippon gives them squads of ninjas as a Special choice whose main strength is mobility, and individual elite ninjas as Hero choices that function like Dark Elf Assassins.
All 'proper' ninja (not counting changelings et al.) in Magic so far come from the Betrayers of Kamigawa expansion set. They all have the ability (known, of course, as ninjutsu) to pop into play by replacing an attacking unblocked creature on their side plus a variety of followup abilities that trigger off of their dealing combat damage to a player. The implication of this is that an individual ninja can masquerade as absolutely anything, from a flock of squirrels up to an Eldrazi. Talk about Paranoia Fuel...
The Complete Adventurer expansion for Dungeons & Dragons (3.5e) features the Ninja base class. They are a viable alternative to the traditional Rogue, trading in more efficient sneak attacks and extra skill points for supernatural dodging and, at higher levels, the ability to turn invisible or incorporeal for a short duration.
The 3.5 splatbook Tome of Battle gives us the Swordsage, a highly versatile class that can fulfill many roles in a party, their most common role being that of a secondary meleer. They have plenty of maneuvers to help with whatever concept you could try to make, and one of the easiest is that of being a ninja (Shadow Hand maneuvers, specifically; things like shadow teleportation and precise, crippling strikes are the meat of the discipline). There's even a prestige class for them, called the Shadow Sun Ninja.
Yu-Gi-Oh! contains a whole lot of ninjas. A trio of them even serve as a Shout-Out to Konami's popular video game series Ganbare Goemon.
In Exalted, each type of Exalt has at least one caste that focuses on stealth, deception, and similar acts of larceny. Sidereals fit the ninja archetype best, though, what with their being snapped up and subjected to intensive training within days of Exaltation, their undisputed mastery of martial arts, their residence in a hidden community that most in Creation can't even find, much less enter, and that whole business with the Arcane Fate that makes them all but impossible to track or keep records on (or even, for that matter, remember clearly). The term 'fate-ninja' really sums them up very nicely.
Feng Shui lists the Ninja as a PC archetype. Their Martial Arts skill and Fu attributes are just one point lower than the Martial Artist, and they have the second highest Intrusion skill in the game (the Thief has the highest with a 16 AV). In addition, one of the Fu paths of the game, the Path of the Shadow's Companion, is tailor-made for the Ninja, with powers that allow you to make silent martial arts attacks and bypass the Toughness of your opponent when attacking someone unawares. You also get to fight ninjas a lot as both mooks and named characters.
The Scorpion Clan, especially the Shosuro Assassins and Bayushi Ninja Infiltrators, in Legend of the Five Rings. Plays the trope straight and subverts it at the same time: the real assassins rely on disguise to blend into the crowd, while the "typical" ninjas in black pajamas are Highly-Visible NinjaMooks often used as a distraction.
In fact, the ninja mooks are aspirants to be "proper" shinobi; if they can survive trying to be "stealthy" in the worst way possible for a year, then they're ready to learn how to do it right. The books even point out that "ninja" gear, by and large, is completely awful. Never use a ninja-to against a katana, for instance.
One of the books states that all Clans have their own ninja-style groups, like the Daidoji Harriers of the Crane Clan (who focus on guerrila tactics) or the Ikoma Spymasters of the Lion Clan (who focus on information gathering). This despite the fact that ninja are outlawed by Imperial Edict, and thus do not officially exist.
In Shogun: Total War you can hire both ninja and shinobi as strategic units. The game makes a distinction between ninja (who assassinate enemy characters) and shinobi (who are spies, saboteurs and seditionists), although historicaly there is no such distinction. The ninja is also horribly outclassed at his job by the Legendary Geisha unit, an ultimate assassin which gets close to the target in her role as a geisha before killing them with concealed weapons, probably much closer to how real-life ninja worked. The expansion also allowed you to train small units of "battlefield ninja", tiny but elite squads which used stealth on the battlefield to get close to the enemy general.
The sequel has the Ninja and Shinobi as the same unit (it's called a ninja but refers to himself as both when clicked) taking over all aspects of spying, sabotage and assassination. The Geisha still exists but is also given a heavy nerf; while she can never be caught and killed during a failed mission, she's much more expensive, easier to spot than a ninja and just as vulnerable to enemy Metsuke. Also, the building that recruits geisha also allows for recruitment of rank 2 ninja, which when constructed in a ninja speciality province like Iga allows for rank 4 ninja straight off the bat, which horribly outclass the Geisha. Battlefield ninja, called Kisho Ninja, also exist, and are the speciality of the Hattori and Tokugawa clans.
Fall of the Samurai flips the whole thing around a bit further. It doesn't even have ninja agents, instead having the shinobi agent fulfill the same role as the ninja has in the base game. It really doesn't differ all that much from it's core game counterpart, the core difference being that it has a slightly different skill tree and retainers. Oh, and the kisho ninja units are still around and recruitable by traditionally focused daimyos.
One of the more interesting portrayals in recent memory comes from a level of the video game Elite Beat Agents. It starts as a subversion: Ken Ozu, lazy heir to a car company, is forced into a ninja outfit by his father and forced to retrieve stolen automobile plans from a rival company, despite having little to no talent. After this, however, the player's success (or lack of) determines what happens. If the player fares poorly, it remains a subversion, as Ken fails miserably whenever called upon to use his "ninja powers". If the player does well, however, it becomes a Double Subversion, as Ken runs smoothly through the "classic" ninja abilities and completes his mission.
Speaking of Andy, he's pretty visible himself in that bright white outfit and his long blonde hair. And doubles as a McNinja, since he's originally from Southtown.
Eiji Kisaragi is a more traditional example, hailing from a remote region of Japan and enters the King of Fighters to settle a grudge against the Kyokugenryu Team. Though he and his team end up being a comedic group of ineffectual"villains".
Spinoff Maximum Impact 2 introduced Nagase, another Highly-Visible Ninja described in-game as "The Ninja Computer Geek".
Samurai Shodown had a number of them, the most typical one being Hattori Hanzo.
Hanzo also appears as a ninja in the Samurai Warriors games. In the first game he was contrasted with Sanada Yukimura in a "ninja vs. samurai" way, but in the second game he's contrasted with Fuuma Kotaro, another ninja, in a similar way to their World Heroes counterparts. The other ninja is Kunoichi, an original character based on the Sanada Ten who supposedly did Yukimura's dirty work for him (subverting his own archetype).
Samurai Warriors 2 adds Fuuma Kotaro and Nene, although the latter is a samurai's wife whose "ninja-ness" is in being a gameplay replacement for the removed Kunoichi. (acknowledged by Hanzo, who, if they meet in one stage, would comment on her having gotten stranger, "since the last time we met.")
Hattori Hanzo was an actual legendary figure in Japanese history, rumored to have been a ninja as well as a pretty decent soldier.
Then there are Sogetsu & Kazuki Kazama, and their magical.
Altaďr from Assassin's Creed I fits the MO of a historical ninja in that he is an assassin who escaped notice by blending in with a crowd, but lives in crusade-era Israel rather than feudal Japan.
Ezio in Assassin's Creed II is more or less the same, only he can swim, is Italian and FABULOUS!!
YMMV. Altaďr is based on the actual group where the word "Assassin" was derived from. There are even several events in the game based off of stories about that group. On the other hand, that group acted far more like the Ninja trope than historical ninjas actually did.
Ryu Hayabusa from the Ninja Gaiden and Dead or Alive franchises. The latter series has a few others, including Kasumi, Hayate, and their half-sister Ayane. Hayabusa in particular has the distinction of being known as the most famous videogame ninja in the eyes of many video game players and is the God of this trope in this site.
A certain not very good Neverwinter Nights module had the player as part of a sect of female ninjas called Kunoichi (which happens to be a historically accurate term for female ninjas).
The village of Mizuho in Tales of Symphonia and its successor the village of Japoni from Tales of Phantasia are hidden ninja villages. Sheena, one of your party members, is from the former, and in the remake of Phantasia, you can get Suzu in your party from the latter.
In no particular order from Mortal Kombat: Sub-Zero, Scorpion, Reptile, Noob Saibot, Kitana, Mileena, Jade, Chameleon, Khameleon, Cyrax, Sektor, Smoke, Ermac, Rain and Frost. Fifteen ninjas in the course of one very ninja-happy series.
Technically, Sub-Zero's clan are the Chinese warriors that Japanese ninja ripped off, and they hate being called ninja. Not that it stops anyone...
Technically, only Scorpion is a ninja. Sub-Zero, Noob Saibot, Cyrax, Sektor, Smoke, and Frost all belong to the Lin Kuei. Jade is Kitana's bodyguard, who is a princess, and Mileena is a clone, both of whom would likely be trained in some form of self defense. Rain, also royalty, is also likely trained in self defense and Reptile is another bodyguard. Ermac might count just from the sheer amount of souls he is made with, probability might dictate one of them was a ninja in life. Chameleon may too, I don't know his backstory well, but Khameleon is just a warrior as well. Most of them are made fairly moot anyways, as only Scorpion and the Lin Kuei are from Earthrealm anyways.
Mega Man 2: Metal Man is also dressed like a stereotypical ninja, though instead of shuriken he hurls sawblades.
You can become a Ninja in Mega Man ZX and its sequel, by obtaining Model P or copying its data.
Mega Man ZX Advent gives us Siarnaq, the one holding Model P (And that you later copies the data thus gaining his powers. His voice is robotic and monotone, kind of reflecting how a shinobi should control their emotions... That is, until you hear him laugh. Perhaps it has to do with him being betrayed by his friends and left for dead in his past?
Sam Fisher in Splinter Cell is repeatedly confused for one by guards. Might go to the point of a running gag as whenever the topic is brought up in conversation the other guard calls them an idiot saying they don't exist. Possibly played for laughs as interrogating a certain guard will prompt him to ask you to kill him with your blowpipe.
At one point in the first game, Lambert explicitly refers to Sam as a "SIGINT Ninja".
Guild Wars has ninja as well in the form of the Assassin profession. Their primary weapon consists of a pair of daggers, they can vanish in a puff of smoke and instantly reappear at at different spot, and they have a variety of spells that fit with the media portrayal of a ninja.
The Dark Templar of Starcraft are Alien Ninjas who can bend light to make themselves invisible.
Kisuke from Muramasa The Demon Blade is an Iga clan ninja. This is notable because Iga was one of the actual places in feudal Japan where there actually were shinobi clan.
The Komoris in Red Steel are a clan of ninjas who fight with guns and poisoned swords, and yes, they wear the stereotypical black pyjamas. Scott himself gets to undertake some ninja training over the course of the game.
There are ninjas in Mad Karate Man that serve as obstacles to prevent your revenge against businessmen from being fulfilled. You can just click them away though.
The WarioWare games have Kat & Ana, twin ninja preschoolers!
A good number of ninjas feature in the Suikoden gameverse, most of them being more visible than not.
Mass Effect 3 brings us Cerberus Phantoms, which are ninjas armed with insanely sharp wakizashis and are protected by barriers. There's also Kai Leng, who's basically the boss version of a phantom.
The Soul Series gives us Taki. She's got the kunai/tanto/wakizashi, uber-agility and magical demon-sealing powers. Plus the purple skin-tight bodysuit.
Also, the "create a character" in 3 had a class called "ninja" that could learn how to wield kuni (with use of ninjustu) , a katan and over sized shuriken (blatant use of jumping and the overly large throwing tool), a sickle that seemed to have been the love child of Ivy's whip blade and a chain whip with some sickle thrown in as an afterthought, Taki's moveset, and (the closest to actual ninjaness) Setska's parasol with a blade hidden in the handle of it. Any character creation after forwent any movesets only available to custom characters, so they then had to use character weapons.
In the Street Fighter series, Guy uses traditional ninjutsu with street fighting influences, Geki and Ibuki fits the popular image of a ninja, and Vega mixes savate and ninjutsu.
In Sengoku Rance, ninja units are among the various types available. While they generally have high Search stats (making them useful for strategic sabotage), they're also effective at tactical sabotage and assassinating enemy commanders in battle. They're not very effective toe-to-toe against warriors or foot soldiers, though.
Shinobi from Red Alert 3, who can throw Shurikens, smoke bombs and kill with a single sword blow.
In the Sonic the Hedgehog series, Espio the Chameleon, ever since the Chaotix crew's return in Sonic Heroes. Complete with invisibility powers and giant shuriken.
Rogues of World of Warcraft can do things like turn invisible, flash step, walk on water, and pick locks. They also make use of intangibility, smoke bombs, poisons, and countless dirty tactics.
The Scyther, Nincada, and Shelmet lines from Pokémon all have ninja motifs. Curiously enough, they are all also Bug-type Pokemon (Scyther=praying mantis, Nincada=cicada, Shelmet=snail) as well.
Koga, the Poison-type Gym Leader from Pokémon Red and Blue, has a ninja motif as well. He's training his daughter Janine in the art, and when he makes it to the Elite Four of the Indigo League in Pokémon Gold and Silver, she takes over the Gym.
Plus, in Hoenn and Sinnoh there are several kid ninja trainers running around.
"I am one of the Ninja Trio! Being discovered means I must battle!"
Kalos introduces the franchise's strongest Pokemon example in the form of Greninja, the final evolution of the region's Water starter. It learns every single ninja-esque Pokemon move naturally (Smokescreen, Double Team, Substitute, and Spikes), along with having two new signature moves (Mat Block and Water Shuriken) that are also ninja-inspired.
You'll get a Ninja no matter what Branch you go on in Vanguard Bandits. What type of ninja they'll be is path-dependent though.
Though they're technically not ninjas per se, the armor for the Dark Brotherhood in The Elder Scrolls V: Skyrim certainly looks the part. The Brotherhood's signature skills also mesh fairly well with the assassin part of the trope.
Aztec Wars has Ninjas, clad in blue, as one of the Chinese units (supposedly, the Chinese empire in the game has conquered most of Asia). They're the basic infantry unit, and they fight with martial arts.
Kaede in Duel Savior Destiny is a ninja and ridiculously formal, for which she gets mocked quite frequently. To Taiga's disappointment, ninjas from where she's from don't employ kunoichi, making her just a normal fighter instead of allowing him to have the sexy fun times he would like.
Cactus, the author of the game, seems to like ninjas. Ninja Flu features another one, this time wearing a missile launcher on his back, to destroy the falling bird flu-infected ninja angels (yeah, his games are weird sometimes). Saru Ga Daisuki features a ninja monkey as its protagonist, with a grappling hook-like tool and the ability to climb walls and ceiling, and a more regular, human ninja who can run and make really far jumps.
Shadow Warrior features ninjas as basic mooks; unlike most ninjas, they wear nothing but pants and shoes and tend to use firearms, though they toss shurikens as well sometimes. They also seem prone to committing suicide for no reason. Some of them are almost invisible.
Bad Dudes features ninjas as enemies who kidnap the President of the United States.
The very obscure Return Of The Ninja is a Spiritual Successor of Tenchu in Game Boy Color, having you sneak through stages to avoid the next screen being filled with mobs and losing rank points for being detected. A Shout-Out it makes to Tenchu comes in the cards you receive after completing the stages or trading with a friend, where some cards makes visual reference to tools you use in Tenchu.
La-Mulana's Kosugi family are descended from ninja; Shawn, Lemeza, and Lumisa all use ninja infiltration techniques to investigate ancient ruins, and it's implied Shawn's father did as well. There are also more stereotypical ninja enemies that appear suddenly, attack, and vanish just as quickly.
Though they are not seen in-game, the player character in Tropico 4 can hire ninjas to infiltrate a heavily-guarded fortress in Tibet. Unfortunately, the price for genuine Japanese ninjas is too high to afford, so the player hires Chinese ninjas instead.
League of Legends features the Kinkou Orders, ninjas dedicated serving the balance of power. They consist Shen, Akali (a kunoichi) and Kennen (a yordle), and all of them are playable to varying degrees, Akali serves as a traditional assassination-based Ninja, Kennen is more about blasting your enemies with lightning, and Shen is an unusually tough ninja that is capable of tanking while having a body built more like a traditional ninja (not very big). They also get their Arch-Enemy, shadow-based ninja named Zed.
Hsiao-Lan, as well as Rapunzel/Hotaru in Rose Guns Days have a similar role, the latter's being close to that of the kunoichi.
And then there's the the title character of the SNAFU Webcomic, TIN: The Incompetent Ninja who takes incompetent to it's logical extreme and is able to commit unbelievably violent acts to anyone except his target.
The Adventures of Dr. McNinja's titular Dr. McNinja, as well as his mother, father, and brother. There are other ninja in the plotline too, but they're less prominent.
The obscure, unknown webcomic Dreamaniac has resident ninja Andrew (who's actually from Switzerland and his younger brother, ninja-in-training Mark.
Freefall had an arc involving a restaurant run by French ninja who would deliver food to your table without you ever noticing, with the nod to real ninja invisibility noted in the trope quote.
Megatokyo features Junpei, nowadays a l337 ninja, thanks to his training under Largo.
Ninjas appear a few times in The Order of the Stick including a half-orc ninja who falls for Elan. A Running Gag is for ninjas to go undetected by other characters even when they're not actually hiding.
Ninjas play a large part in the final arc of Buck Godot, because every race in the known universe has them...
SPRINGIETTE features Chop Chop Ninja Doom, who throws chips instead of stars.
Teenage Mutant Ninja Turtles: The fab four have been been kickin' shell on weekday afternoons and Saturday mornings since the mid '80s. They started as traditional ninja, by operating in secret or under the cover of darkness, but it wasn't look before the people of NY knew about them. Now? Depending on the series and the setting, they're either adored by the public or they're misunderstood.
Kim Possible is infested with them: a few one-shot bad guys, some specialized "embarrassment ninjas", a secret ninja high school where Ron spent a week as an exchange student, and of course Monkey Fist's ninja clan made entirely of monkeys.
In Jackie Chan Adventures the Shadowkhan, a milita of demonic ninja, were often deployed by the bad guys to fight Jackie. Season 4 featured nine different groups of Shadowkhan.
It took four seasons before Samurai Jack fought a ninja, but he did - a robot ninja at that. It was, at least, a stealthy one, made completely invisible whenever it stood in shadows. And then Jack revealed he could do the same trick with sunlight, leading to one of the most visually incredible fights in the series (which is saying something), as the series is made of cool.
Transformers Animated has Prowl and Jazz as goddamn NINJA ROBOTS. How much cooler can you get? Ironically, Prowl's a pretty honourable guy as a ninja (as is Jazz) but the moment he puts on the Samurai Armour Upgrade, he becomes a totally arrogant asshole one step away from turning into a villain.
Prowl was slightly arrogant already, as he seems to think a lot of his own abilities. This is tempered by the fact that he actually just is that badass.
Animated went on to reveal that there's an entire order of ninjas back on Cybertron, which includes Animated versions of almost every Autobot martial artist, melee-weapon user, fist fighter... and Grandus.
The short Australian CGI spoof Samurice. Ninja Rice steal the sacred Soya Scroll, and samurai hero Ricesashi has to get it back.
In an episode of Thundercats, Mumm-Ra summons a samurai named Hachiman and tries to trick him into fighting Lion-O. When that doesn't pan out and one of his minions is captured, he tries to salvage the situation by doing the unexpected: Summon a ninja.
Monkian: I don't see anyone!
Mumm-Ra: Look behind you.
[Monkian looks behind himself, only to fall over in surprise.]
Mumm-Ra: This... is the NINJA! If the samurai has all honor, then the ninja has none. His methods are silence, secrecy, and stealth. And his weapons — dagger and disguise...
In Avatar: The Last Airbender , Katara and Zuko dress in all black and stealth their way around several Fire Nation navy commands, seen by no one until they attack, in order to get information on the man that killed Katara's mother. It's all kinds of bad-ass.
The Dai Li are Earthbending Ninjas. While they don't do the all black attire normally attributed to the profession, the training and combat style they use fits the bill perfectly. Unlike most Earthbenders, or any capable bender in the series, they use hidden weapons and misdirection in their combat style.
Also, Zuko in Blue Spirit mode. Silent, stealthy, wears all black, incredibly badass, one of the only characters to be actually deadly in each appearance... total ninja right there.
The Equalist chi-blockers in Legend Of Korra are stealthy mask-wearing fighters that use a pressure points to disable benders alng with bolas and smoke bombs to throw their opponents off balance. True to the idea of ninja, they also don't care about fighting fair, though when your opponents have Elemental Powers you need every advantage you can get.
Kabuto, the main villain of ''Tokyo Mater'' has ninja racing cars for henchmen. He summons them to distract Mater about halfway through the short, only for them all to be knocked out by Dragon McQueen. At the end of the short, Mater wins the race, and since Kabuto threatened him that if he lost the race, he will strip Mater of his modifications, when Kabuto lost, he is stripped of his own modifications, and is laughed at by his own ninjas who then turn to the side of Mater, now "King of all drift racers."
Transformers Prime has Wheeljack. No longer a wacky scientist with a penchant for inventions that blow up. He's now a badass ex-Wrecker ninja with a pair of laser-deflecting katanas and a mask to boot. Not to mention quite cocky.
Starscream: "Do you not see that you are vastly outnumbered?"
Wheeljack: "I see fellas who might vastly enjoy watching me pound some dents into you."
Yoshi and Akiko's mother, Mrs. Yashida who sneaks into the Smith's home dressed to rescue her daughter being held prisoner by Francine so Steve can win a spelling bee. She knocks Hayley unconscious with a dart.
Ninja can catch arrows in flight - BUSTED! Guinness Book Of Records champion ninja, they shot safety arrows at him. 6 arrows hit him. He jumped away from 3 and caught the 10th arrow; in a real fight, he would have been dead before that 10th arrow.
Ninja can lie in a carp pond all night breathing through his blow-pipe and when the victim goes for a morning stroll, shoot him with poisoned darts. PLAUSIBLE. Using a blow-pipe underwater takes a bit of practice, but is doable. Tory managed to stay under cold water for one hour.
Ninja with sword versus archer 30 yards away. Archer shoots. Ninja knocks away 1st arrow with sword and charges before archer can reload. CONFIRMED! Jamie guessed he could have reloaded if the distance were 100 yards, but they never tested it.
Similar to MythBusters, the show Fight Science also did some work with ninja (also special ops of various nations, and fighters from other schools).
They proved that ninjutsu really does have a deadly punch (compressing the rib cage enough to cause fatal damage to the heart).
Some of the more infamous ninja in history (and some folklore) especially originating from Jidai Geki:
Hattori Hanzo, the Miyamoto Musashi equivalent of ninja, was a part-time ninja: as an Iga retainer in service of the Tokugawa dynasty, he was seen as a retainer with an exceptional special skillset and tactical bravado (earning him the moniker "Devil Hanzo")— however he was also reknown for swordsmanship excellence, and skills with a spear. His appearance as a ninja nowadays is probably a direct result of his tactical choices that earned him his "Devil" nickname; tactics along the lines of subversion, misinformation, assassination, etc.
Sarutobi Sasuke, one of the men counted as The Sanada Ten Braves. Bodyguard of Sanada Yukimura. Granted his name to five ninjas in Naruto: Hiruzen Sarutobi the Third Hokage and his father, Sasuke; Konohamaru Sarutobi, who is basically Naruto's apprentice; Asuma Sarutobi who is Shikamaru's sensei; and finally Sasuke Uchiha himself.
Although, it is rumoured that Sarutobi was a fictional character, or at least a fictional name tagged to label a certain ninja that may or may not have been serving Yukimura.
Fuuma Kotaro, Hojo's ninja, most famous for that myth about him luring and killing Hanzo in a naval battle, suicidally.
Mochizuki Chiyome, Takeda ninja and credited as the founder of kunoichi.
The Sulsa, the ancient Korean equivalent of the ninja.
The SAS, Navy SEALs, Spetznaz etc. are ninjas in all but name. And ninjas are part of SPECWARCOM in all but name (and time period).
Masaaki Hatsumi, who claims to be part of the last remaining ninpo lineage. And yes, they wear the black pajamas. They also wear pajamas in various colors that fit the environment.
Ninja schools exist, even in America. They're usually specifically trained for the army.
Besides Ninjutsu, there is another (and uniquely American) martial arts style developped for use in hand-to-hand combat. It's called MCMAP (Marine Corps Martial Arts Program). You won't find schools in shopping centers that teach MCMAP, though, as only members of the US Navy or Marine Corps are permitted to study MCMAP. MCMAP is unique in that it is the only style in which people train in full combat gear, including training in the use of pocket knives and bayonets as offensive weapons (as opposed to something you might disarm an enemy of and use it against him). Basically, it's Ninjutsu adapted to modern combat.
There's also the Bujinkan system which teaches unarmed and armed combat techniques from Ninjutsu while omitting the stealth and infiltration training. One of the more prominent teachers of the school, Stephen K. Hayes, since removed from the rolls, is famous for having released a number of "how to" books on Ninjutsu.
Though Bujinkan may not truly be derived from martial arts used by ninjas, as Ninjutsu is not a martial art (such as karate or taekwondo), despite what many people think. The art of Ninjutsu consists of guerrilla and espionage strategies; and not head-on combat techniques.
Ashida Kim is a self-proclaimed ninja who is based in Lake Alfred, Florida. Having written over 30 books on the subject, he claims to have learned his ninjitsu from someone named Shendai. He also claims to have met Count Dante (who is best known for his "Deadliest Man Alive" ads appearing for years in comic books) and trained under him. He also has posted a $10,000 challenge to anyone who wants to fight him. It should be pointed out that the aforementioned $10,000 is not awarded to the person who defeats Kim. It is Kim's fee (plus travelling/lodging expenses and a $25,000 appearance bond assuring the challenger is "serious") for showing up to the fight. Long suspected to be the pseudonym of a Christopher Hunter, recent investigations have suggested that Ashida Kim's birth name is Radford Davis. Also, despite the Japanese first name and Korean last name of his favorite alias, Mr. Davis is very caucasian.