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A villain whose main, often hidden, motivation is that he feels incomplete. This character is ashamed or enraged at the thought that he was seen as obsolete or surpassed by someone in front of him. This can be anything from a teacher who found a new student to a scientist who builds a "better" android, and is a common tragic fate for a Replacement Goldfish.
In the android/clone/other doppelganger scenario, the typical reason for this assumption is that the character lacks some vital component to be truly great or human, and might even be considered dangerous because of the lack. The typical subversion is that the original was too willful and independent, and subsequent models were made much more compliant.
If this "second model" is one of the heroes, the original's feelings may grow into an obsession with beating the newcomer and proving he's the best. The most humiliating defeat he can have is usually being shown that he was an Ineffectual Loner.
This kind of character is often The Resenter.
See also: Broken Hero, Psycho Prototype, Replacement Goldfish, Cloning Blues and Flawed Prototype.
Not to be confused with a Dummied OutMook in a video game.
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Suigintou from Rozen Maiden, who, in the anime, is literally incomplete.
"Copy Rezo" from Slayers, who spends his entire, brief life trying to outdo the original Rezo. He is greatly angered every time someone mentions that he is "just a copy".
In Fullmetal Alchemist, this is the reason why Envy hates humans; they can overcome obstacles because of their tenacious spirits, and they have the love and friendship of those around them. Eventually this causes him to commit suicide. Really says a lot about the homunculi's family dynamic.
Several of the homunculi in the 2003 anime are motivated by a desire to become fully human, and will do anything they feel will further this goal. Lust explains that without a human soul, she feels incomplete. Envy in particular burns with a fanatical desire to personally murder his creator for this feeling. There's also a lot of friction between lesser homunculi and the "better" versions, who can more convincingly pass as human.
Dr. Hell from Mazinger Z has shades of this. Part of his animosity and resentment towards Dr. Kabuto comes from the fact he thinks Juuzo surpassed him, rendered him obsolete and took all away him when they were younger: due to his crappy childhood Hell threw himself into becoming a scientist in order to standing out. When he was a college student people still shunned him but they respected he was the top student, and he prided on that. However Juuzo quickly replaced him, and he also earned the heart of the woman Hell was infatuated with. All of it contributed to the breakdown turned Hell into a Mad Scientist. And in the third episode of Mazinger Z, after his first batch of Mechanical Beasts were crushed by Mazinger-Z, Hell got a Villainous BSOD due to after fifty years, Juuzo Kabuto STILL could surpass easily whatever Hell did.
Not a villain either, but one of the reasons for Asuka's breakdown was being a Humongous Mecha pilot was all she thought she had, so she worked hard for one decade to become the best... only to be surpassed and beaten every turn by a meek kid that, as far as she knew, they picked up from the street, making her feeling useless and worthless.
Tekkaman Evil in Tekkaman Blade is the main character's identical twin brother. He's got a hell of a brother complex - in addition to ridiculously amplified sibling rivalry, he's also decided that the world can only handle one of them and that it's destined that one will kill the other. These motivations are greater factors in his drive to kill Blade than alien possession.
In GUNNM ( Battle Angel Alita ) Last Order, the android AR Six is, when we first meet her, driven to prove her worthiness as a lifeform by destroying 'the original' from whence she came (Alita herself).
Cell from Dragon Ball Z, despite claiming to be the pinnacle of Dr. Gero's genius.
Ulquiorra from Bleach is hinted to have this motivation, since he always pierces "interesting" opponents in the same place where his Hollow hole is located.
Ranban from Space Pirate Mito was driven to perform a coupe d'etat in the form of blowing up an entire planet and taking over the Galactic Patrol due to the fact that he was imprisoned because his body never settled on a gender (his species is gender neutral until puberty).
Blackwargreymon from Digimon Adventure 02, being created from nothing but strands of the current Big Bad's hair combined with the remains of the preceding Big Bad's control spires has this problem. Much of the drama of his story arc comes from the protagonists trying to convince him that no matter how he was born, he's certainly a real person now.
Twisted in Mermaid Melody Pichi Pichi Pitch. Though the Winged Ones don't honestly seem to care that they're only replicas, when Michel kills them, he tries to tell them that they're worthless because of it. They respond by revealing, as they die, that he was a clone too, only raised to believe that he was the genuine article. Cue Villainous Breakdown.
Canard Pars in Gundam SEED X Astray. Everything he does is motivated by the fact that he was discarded as a "failed" prototype of Gundam SEED protagonist Kira Yamato. Canard wants to kill Kira so as to prove he's not a failure. Ultimately, X Astray's protagonist Prayer Reverie dies saving Canard, triggering a Heel-Face Turn. Canard later sees Kira in person for the first time, and walks away.
In the Gundam SEED anime, Big BadRau Le Creuset is a failed clone who has the face of a man who abused him by tryiing to force him to become an extension of his own ego. Lacking any sense of identity, the clone becomes The Resenter towards the entire human race, and Kira (a successful genegeneering project) and La Flaga (his father's biological son) in particular, ultimately going into Omnicidal Maniac territory. In Gundam SEED Destiny, Le Creuset's clone Rey Za Burrel tries to live out a better version of the former's life, for similar reasons.
Shagia and Olba Frost from After War Gundam X are a pair of Category F Newtypes who were rejected by the government because their Psychic Powers weren't strong enough. They're now planning to kill every Newtype in existence to prove their own value.
Death Note's Mello and Beyond. Mello join the mafia and confronts Kira because he wants to surpass Near, because he thinks Near is a more perfect successor to L. The latter's entire motivation for killing 3 people and setting himself on fire is to beat L as a criminal, since he could never beat him as a successor.
Angel Sanctuary: Plays heavily into most of the angels, both the good and the bad. *deep breath*
Lailah aka Sevothtarte was a brilliant scientist, but she was also relatively plain, and never matched up to her superior Anael. When she finally got her chance to shine, jealous co-workers raped her. Although she killed them in self-defense and scapegoated Nidhogg for the deed, she was still branded a fallen angel, which left her so emotionally shattered that she sold herself to Sandalphon to escape from her past. Though she believes (as Sevothtarte) that she's safe from her past, her actions give her insecurities and self-loathing away constantly.
Kabuto from Naruto tried to find out who he was this way.
In the Mortal Kombat comics, this was the modus operandi of Kintaro, who felt inferior and "living in the shadow" of his prince, Goro.
Also in the games, Sheeva had shades of this trope, after her Shokan race was replaced as Shao Kahn's chosen warriors by their mortal enemies, the Centaurians, despite being given other, equally important jobs (like protecting then-resurrected Queen Sindel).
Marvel Comics' X-Force gave us a Beta Test Good Guy in Cable, the scarred cyborg soldier. He had gone through life assuming he was a flawed clone of Stryfe, who had strong telekinetic powers and insanity to match. He eventually found out he was wrong: he's the original, Stryfe's the clone.
The Vulture went into a life of crime when he was screwed over by his younger, more savvy business partner.
Superboy of the Teen Titans slips into this feeling now and then.
In Final Fantasy VII: Advent Children, Kadaj and his brothers are "larval" forms of Sephiroth, who need Jenova cells in order to completely "mature", not that it's ever entirely clear why they exist in the first place.
Word of God has explained these are literally incomplete copies of Sephiroth. He tried to reincarnate himself in full, but he wasn't strong enough and had sacrificed too many of his memories to keep himself alive in the Lifestream to create a perfect copy. So he created three copies that were as close to him as he could get with the memories of himself that he had to work with: Loz is his strength & masculinity (completely ignoring his crying fits), Yazoo is his cruelty & "enigmatic allure," and Kadaj is his insanity & childishness (which is notable in that Kadaj is the only one who shares the original's cocky refusal to use firearms).
Hojo also mentioned something about Sephiroth clones in the original Final Fantasy VII.
That is actually a huge misnomer. The "clones" are simply individuals from Nibelheim put through the SOLDIER procedures—the main (and eventually proven meaningless) difference being that Sephiroth's cells were used, rather than Jenova's. Hojo only did it to prove his Jenova Reunion Theory and to see if more people with Sephiroth's unusual powers could be produced (as we all know, they couldn't). This is probably the reason why the term "copies" was used in Crisis Core, rather than "clones."
A Mexican movie called "Una película de huevos y un pollo" ("A movie of eggs and a cock", innuendo made completely on purpose). The bad guy is a stone egg who needs a chicken's heart to make a spell to have feelings.
Mewtwo's circumstances in Pokemon The First Movie are much the same as Blackwargraymon's in the Digimon example above; he was cloned from Mew's DNA in a lab, and spends the majority of the movie railing against the implications of his origin. His eventual Heel-Face Turn is triggered by the revelation that the manner in which one came to be is not as important as what one does with the life they have.
G.I. Joe: The Rise of Cobra has the evil ninja, Storm Shadow. Backstory shows he perceived his Mentor showed too much favoritism towards Snake Eyes.
Frankenstein's Monster: In the original book, his murderous rage is fueled by being alone and universally hated on sight. He was fairly content until he discovered that everyone he met was horrified at the sight of him. He wanted company, and his creator refused to provide any. He's written as an intelligent and compassionate person at first, but becomes a nameless victim of What Measure Is a Non-Human?.
In Gregory Macguire's Wicked, it is suggested that Elphaba's more villainous deeds were motivated by her belief that she lacked a soul.
Actually quite a big theme in the book, as opposed to the Musical's Beautiful All Along theme. It links back to the Animals, and how they're considered inhuman, thus soulless, despite being sapient. Also notions that the reason the water killed her is because it was a symbolic baptism, that is, her acquiring a soul.
Older Than Feudalism: In The Bible, Cain slew his younger brother Abel because he was jealous of Abel's sacrifice receiving greater praise from God. "The Lord had regard for Abel and his offering, but He did not have regard for Cain and his offering. Cain was furious, and he was downcast." Genesis 4:4-5.
Live Action TV
Heroes: Sylar's motivation for being a superhuman serial killer is that after his parents forced him into a boring, menial, unspecial job and he was let go by Chandra after Chandra concluded that Sylar wasn't special, Sylar wanted to be special. His idea of special just happened to be having every power he can get his hands on.
Sylar is a good example of both how pathetic and how dangerous a villains like this can be, since the sense of incompleteness that drives them probably won't go away no matter what they do and no matter how much of their goals they achieve - which means that they'll never, ever stop. There aren't enough powers in the world to make Sylar as "special" as he thinks he needs to be. Too bad that There Are No Therapists...
Knight Rider featured not one, but two examples of this trope. KARR, the Evil Twin of KITT, was a flawed prototype that was mothballed for its indifference to human life, and harbored a lingering resentment against its creator and its replacement, which it called an "inferior production-line model." Garthe Knight was disowned by his father when he became a criminal, and later replaced as Wilton Knight's heir and son by series hero Michael Knight. Michael's face, which had been destroyed by a gunshot, was also reconstructed in Garthe's image. Garthe always bore a lingering resentment against Michael, who he considered a usurper and an inferior copy.
This is a bit of a subversion, though, because the Replicators who actually care about ascension aren't the bad guys. Played straight, however, since the reason that most of the Replicators hate humans and want to destroy them is because of their jealousy over being neglected by the Ancients.
The android Lore from Star Trek: The Next Generation, who was literally the initial model replaced by his android brother Data. A textbook example of the trope. Ironically, Lore had emotions from the start, while Data started out as mild mannered artificial intelligence incapable of truly experiencing or understanding human emotions and longed to have them (classic Pinocchio Syndrome). Data once even told Lore that he "envied" him. Lore on the other hand lacked something Data was programmed with: a conscience. Lore murdered their creator, Dr. Noonian Soong, because he felt "daddy" loved Data more.
In the TV series, Dr. Soong himself said Lore was the earlier model. Later Star Trek episodes suggested that there were previous models that didn't even get to Lore's sophistication (or crashed and burned before getting a chance to develop). The tenth movie Star Trek: Nemesis introduced one of these named "B-4", who only had a very crude artificial brain.
In the re-imagined Battlestar Galactica, Cylon human model number 1 John Cavil believes himself to be inferior to the robotic versions, which pisses him off to no end ("I want to see dark matter!").
BIONICLE has the plant monster Karzanhi, a prototype for the Morbuzakh. It felt that its form was inferior, and requested that the protagonists bring it some Mutagenic Goo in exchange for The Cure for Nokama's poisoning.
Fear Factory's entire discography consists of science-fiction concept albums full of songs which describe this trope in agonizing detail, from the first-person perspective of clones, androids, and cyborgs "born" into a world that doesn't need or want them, a world consumed by a war of man-vs-machines. Prominent examples include "Replica" from Demanufacture, and "Descent" and "Resurrection" from Obsolete.
Copy X from Mega Man Zero, who was built as a replacement for the original Mega Man X. He was built in order to prevent the people of Neo Arcadia from noticing that X was gone, and decided the best way to end the fighting between man and machine that had been going on for the better part of 200 years was to enslave all Reploids and annihilate the ones that resist.
Dr. Wily from Mega Man Battle Network lost his robotics research's government funding to Dr Light Hikari's network research, making him bent on world domination in order to get revenge on the society that ignored his robotics research
Also Proto Man - he's essentially a prototype of Mega Man with an unstable reactor and a bit too much free will. Not technically a "baddie", but one would easily be forgiven for believing him to be a baddie after playing Mega Man 3 but not finishing the game (or watching the Ruby-Spears cartoon).
Wodan Ymir from Super Robot Wars Original Generation 2, an artificial being from an alternate universe who was made from the corpse of the alternate version of one of the heroes of the game, Sanger Somvold. Similarly, Lemon Browning was made from the corpse of the alternate Excellen Browning.
Duminas from Super Robot Wars Reversal was a monster created for an unknown purpose. Her creator decided she was a mistake and tried to kill her, but her creator was killed in response. Duminas then spent the entire plot trying to go back in time and ask him why her creator called her a 'mistake', so she could fix herself. Along the way, she made three creations of his own, but she showered them with love. Upon her death, one of the good guys remarks that she figured out what she was... A human.
The Riku Replica created by the Organization in "Chain of Memories". They make him to fight Sora, and give him false memories of being the real deal. When he finds out that he isn't the real thing, he develops some serious emptiness issues. He goes as far as trying to kill the original so that he can be his own person.
Repliku: "As long as you're around, I'll never be more than a shadow!"
The Organization themselves, high-ranking "Nobodies" - empty husks created when The Heartless tear out your emotional core. Most are warped into inhuman mooks with no sense of self, but the Organization retain their human shape and memory, so they know what they've lost. Their members range from conflicted to psychotic, while their leader has no interest in being whole again and just uses hearts as a power supply. 3D adds another twist - they could have regained their hearts without hurting anyone over time, and some of them (Axel, Roxas) showed signs of doing so. Xemnas kept this quiet so they'd be vulnerable to his original self's body-stealing plan.
The fourteenth member of the Organization, Xion (from 358/2 Days) falls into this the hardest, being the focus of her debut game. Played with in that she's a Replica of the series' main character, like the Riku Replica above, and subverted in that she just feigns being a Beta Test Baddie, ultimately turning out to be one of the only good characters in the game.
HK-47 from Star Wars: Knights of the Old Republic has elements of this trope, lamenting his incompleteness in the first game, and outraged that the HK-50's, based on him, exist. Only, he does not feel inferior to them in any way, decrying them as in fact being lesser than he in most respects, such as behavior and, well, color. Even more infuriating, they fall within his I Cannot Self-Terminate programming.
The originally planned ending for KotOR II had HK-47 sidestepping his inability to destroy the HK-50s personally by having an army of other assassin droids do it for him. A later guide book indicates that this still happened despite being cut from the game.
Liquid Snake from Metal Gear Solid probably falls under this. He believes himself to be an inferior clone of Big Boss, and genetically inferior to his brother, Solid Snake, due to having received "recessive genes" while Solid got the "dominant genes". Of course, as it turns out, it was really Liquid who was supposed to be the superior brother, but he doesn't know that. Despite being Nigh Invulnerable, Made of Iron and an Implacable Man, all at once.
And Word of God says that neither of them was the superior one and Liquid apparently just has a shoddy grasp of genetics.
E-101 Beta from Sonic Adventure: replaced on the crew of the Egg Carrier by "younger brother" E-102 Gamma after Gamma defeats him in battle, then scarily remodeled for Gamma's final boss fight. They end up destroying each other, but the good news is that this releases the animals trapped inside them, finally liberating them from the Doc.
In the same vein, E-123 Omega. He was deactivated by Eggman when he started the E-1000 series, was reactivated by Rouge and now spends his time annihilating everything Eggman creates just to prove he's the best of Eggman's creations. The ironic part is that he's a heroic version of this trope... well, mostly anyway.
And of course, Metal Sonic is often portrayed as having such issues. In the Sonic OVA, he eventually destroys himself, while in Sonic Heroes, he's driven to usurp Eggman, take over his army, and use the powers of Perfect Chaos, Shadow, and most of the cast to become Metal Overlord. The twist is that in Heroes, Metal believes Sonic is his copy.
Inverted in Advance Wars: Days of Ruin, where Cyrus betrays his father, which he is a clone of and a failed vessel for a Grand Theft Me experiment, and helps the heroes exactly out of a sense of not being fully human.
Advance Wars: Dual Strike has a similar inverted example to Days of Ruin with the Andy clone. Rather than being bitter about being a cheap copy he asks if Andy has friends and, when told yes, remarks that it makes him happy because he feels as if he has them as well.
In Final Fantasy IX, Kuja the villain is the original and Zidane the hero is the replacement. Kuja goes truly cuckoo after learning that his lifespan was purposely designed to be short as part of the plan.
The Black Mages are also this trope, except that the ones who become self-aware stop wanting to kill things.
I'd actually say they're more of a subversion. Since they aren't self-aware they can't have any motivation, let alone envy of a superior version. They kill things because they are ordered to by their human superiors.
A major inversion, however, is Asch, who himself was replicated and loathes his clone not only because he considers it weak and useless but because it took over his life.
Ramsus from Xenogears initially appears as the Big Bad, although as the game progresses and he gets defeated by Fei and his Split Personality, Id, Ramsus develops an inferiority complex to Fei, going so far as to ruin the plans of one of the game's real Big Bads by ignoring his orders and attempts to kill Fei (he gets completly and utterly trounced, which doesn't help his issues). It turns out that Ramsus was going to be an artificial Chosen One before Fei was born, but after Fei was conceived, Krelian gave up on Ramsus to focus on Fei, which was the initial result of the inferiority complex.
In Deus Ex, Anna Navarre and Gunther Hermann both have mechanical body augmentation, whereas the player character is one of the first agents to be augmented using new nanotechnology. Gunther in particular resents the fact that his generation of augmentations is supposedly being rendered obsolete, although this resentment is probably not his primary motive.
In Beat Angel Escalayer, FM77 is a clone of Sayuka, and wants to defeat her and steal the Doki Doki Dynamo to become "complete".
Double stacked in the Soul Series. Originally, Astoroth is modeled after Rock when he is created, and feels some annoyance at it, and Astoroth being arrogant he wants to prove he is the better despite being modeled, and in IV, a replacement built by the same cult that make Astoroth is sent to kill him and bring back his body due to the fact that he appears to have been able to start thinking for himself. If there was any jealousy between them it's unknown.
One character in Mass Effect 3's Citadel DLC has this motivation. The main enemy is a clone of Shepard, who was created by Cerberus as a spare organ repository for the genuine article.
Subverted in El Goonish Shive, where Ellen was going to be this but became part of the main cast instead because the creator wanted to avoid the Cerebus Syndrome that a recurring villain would entail.
Umbria/Zaedalkaah, from Our Little Adventure. Umbria's main quest is to reclaim her power with 'The Brotherhood' and getting her old body back. The form she is currently using is an imperfect copy of Julie's Bard class and appearance, though Umbria looks little more evil than the original Julie.
A more literal version of this trope occurs in Sluggy Freelance:  Though it isn't a major villain in this case.
In The Gamers Alliance, Rune is an almost perfect clone of the deceased sorcerer Jemuel during the Great War but is annoyed when he is still referred to as a mere clone who hasn't reached the original's potential. He spends his life trying to become more powerful than Jemuel, but in the end he fails miserably although he does cause the reactor core explosion in Libaterra due to his machinations.
Played with in Buzz Lightyear of Star Command. One episode's plot revolves around XL stealing the one part that heroic XR has and he doesn't—by grabbing XR and ripping it out of his chest, while he's still fully conscious. This sends XR into a manic-depressive state over losing this part, as he now thinks he's the worthless one. It turns out the part was a worthless air-freshener device.
Even more so, the air-freshener was only put in because the aliens that had built him could smell an odor. Everyone who worked with him were incapable of noticing the change once the device was removed.
Spider-Man: The Animated Series: Spider-Carnage is a demented Evil Twin of Spider-Man. Hailing from an Alternate Universe he is his world's version of Peter Parker... maybe. An encounter with Miles Warren resulted in Peter (already highly unstable following the deaths of Uncle Ben and Aunt May) being cloned. The clone took up the identity of the Scarlet Spider and became a productive member of the superhero community, while Peter became enraged, feeling that Ben's existence threatened his own. And then The Reveal came in from Curt Connors—Peter might actually be the clone. This news pushes him over the edge, attracts the Carnage symbiote to him, and sends of the path towards destroyingall realityin a Class Z apocalypse.