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Opening a Can of Clones

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In Speculative Fiction, time travel, shapeshifters, robot duplicates, clones, resurrection, alternate universes, and mind manipulation can be exciting and add a layer of ambiguity and suspense to a story. They can fill characters and viewers with paranoia and make for great shocking revelations. However, they can also lead fans into a forest of Epileptic Trees, and in so doing completely derail the story and kill all drama. The problem stems from the possibility that: if characters can be brought back to life, or if imposters, time-travelers, and illusory sequences can be used to unmake plot points at the author's behest, how can viewers be sure that any given story element is permanent?
Or, to put it in other words: Nothing is at stake if there is no guarantee of lasting consequences.
It's an unfortunate outcome of the Second Law of Metafictional Thermodynamics, which dictates that because writers need conflict in their stories, they cannot resist destroying their worlds and killing off characters in order to create said conflict. If they keep doing that however, they'll eventually run out of things to destroy. The author could employ a Time Skip in order to justify reconstructing the world, but doing so would also significantly change the universe (and potentially alienate existing fans who only liked the pre-Time Skip universe). Thus, to keep their world alive without any serious changes, the author opens up the proverbial can of clones. This allows them to walk back their plot points, and in theory, they can keep the story going forever—resetting things every time they run out of characters and worlds to destroy. The problem however is that audiences tend to be once-bitten, twice-shy. After a while, no matter how much the writer insists that this time, honest to God, the character has been Killed Off for Real, the audience will never believe them. And then, the next time a character's life is threatened, the audience won't even care, because they now know that death can be undone.
What happens next is that viewers become skeptical of all the plot devices that merely can be exploited in this manner even the first time they're introduced; especially if the franchise had already gone a fair length of time without them. There's a sort of unspoken assumption that the moment you start resurrecting the dead, travelling through time, or exploring alternate universes, then nothing which happens in your story matters anymore and so the work can only go downhill from there.
A few things that may cause viewers to stop taking your story at face-value:
Bringing characters Back from the Dead. Viewers are aware of the First Law of Resurrection: if an author has already proved willing to resurrect the dead and said author really wants to bring another character back, they will find a way of doing it. Even if it comes at the expense of the story's integrity. Notably, poor use of the Cloning Gambit (which is where the name of this trope comes from) is an especially egregious means of achieving this. Furthermore, if an author makes a given death permanent after already using some manner of resurrection previously, it might cause viewers to become disconnected from the characters, who chose to bring back Character A but didn't bother with Character B.
A Faux Death or Disney Death. Even if the character didn't actually die, it risks lessening the impact of a character actually dying. It's particularly bad if the entity who bit it is an Expendable Clone or Actually a Doombot, or if the circumstances surrounding their fake-out death—as common sense would dictate—should have been completely un-survivable.
Strong as They Need to Be and over-reliance on Plot Armor. If the author relies too heavily on Contrived Coincidences, Deus Ex Machinas, Eleventh Hour Superpowers, Story Breaker Powers, Ass Pulls, or New Powers as the Plot Demands to get the heroes out of danger, the audience is going to stop caring not only about whatever threats they might be facing now, but likely won't even care the next time said heroes' lives are threatened, either.
Excessive tweaks to the continuity. If the author relies too heavily on Retcons, Alternate Timelines, The Multiverse, and Continuity Reboots, viewers are eventually going to stop caring about what happens there. One can try and fix it with an Alternate Universe, but that brings up its own problems: first, such universes can be seen as expendable, and second, it causes Uniqueness Decay—the audience will have a harder time identifying with Alice and Bob if they're not the only Alice and Bob in existence. Either way, it also leads to The Firefly Effect on a continuity level—audiences don't want to get emotionally invested in a continuity which will just get deleted at some point.
Overuse of Time Travel as a plot mechanism, especially as a means of "correcting" dramatic or tragic events which may have happened in the past. Again, it signals to audiences that nothing is going to stick. Granted, a writer can potentially sidestep this issue by creating a Stable Time Loop—thus rendering it impossible for the characters to actually change any past, present, or future events with time-travel—but this solution risks eliminating any notion of free will, in which case the writer must decide whether they're willing to sacrifice characters' autonomy for the sake of tension, or vice-versa.
All Just a Dream, Mind Manipulation, and Hallucinations, which can annoy audiences with even so much as a single use. If you have a character who can change what the other characters perceive (such as a Master of Illusion, a Dream Walker, or a Telepath), the characters can't be certain that what they're perceiving is reality. If the audience shares the characters' viewpoint, they can't be certain of anything either. It can even add unintended extra layers to the audience's doubt—e.g. going from "Did The Hero really just see his Love Interest die?", which the author may have intended, to "Did the Love Interest even exist at all to begin with?", which they didn't.
So we've offered a few ways to avoid this reaction:
Make rules for your universe and stick to them. Audiences are more likely to accept a plot twist if it's consistent with the universe they know. If you're breaking out the mechanism behind your twist for the first time when it's introduced, it looks a lot more like an Ass Pull. If your plot is all about cloning, time travel, mind manipulation, etc., then rules are a necessity - both to keep yourself honest and to establish stakes that will engage readers.
Use those rules to impose limitations. If there are no clearly defined limits as to what a shapeshifter, clonemaker, illusionist, time-traveller or other wizard can do, the audience is going to assume that they'll always be able to change whatever the author wants. If there's a limitation of some kind, however, the audience is going to be on the lookout for the holes in those abilities. It can even add another layer of enjoyment for the audience, as they can try to Spot the Thread (especially if they can do it before the characters). A particularly effective limitation is if It Only Works Once, as this adds dramatic tension and prevents those abilities from becoming a Story-Breaker Power.
Include a Meta Guy or Audience Surrogate, with the same Genre Savvy as the audience. If your setting is established to have shapeshifters, clones, or illusionists, then good world-building would establish that the characters know about these things, too, and would become just as skeptical as the audience. How do high-status leaders like kings and generals avoid being tricked or replaced? They might become Properly Paranoid and prone to mind games with their adversaries, and they may even be able to set up countermeasures to spot fakes like a Trust Password.
Give Shapeshifters and illusory sequences a tell. The characters may not be able to see through it, but at least the audience has a definitive way of determining who or what is real and who or what is not. You could make it very difficult for a shapeshifter to copy someone 100% accurately, either physically or in personality. Or you could have them revert to their true form once they die. Illusory sequences can be given a different visual or physical aesthetic which makes them immediately distinguishable from "real" sequences.
Add ramifications to bringing a character Back from the Dead. If there's a risk that they Came Back Wrong, the character's "death" still has lasting repercussions for the story.
If you insist on bringing characters Back from the Dead, at least establish conditions under which that's impossible and the character is Killed Off for Real. Perhaps you can find a way to make a character Deader than Dead.
If your story involves Time Travel, it is recommended that there be a high risk of unintended and deleterious consequences to its use. If the heroes' use of time-travel is just as much the cause of their problems as it is the solution, that in turn can disincentivize them from using it in the first place, thereby dissuading viewers from suspecting that it will be conveniently exploited to solve any other dilemma which the heroes come across.
If your world is intended to be in flux (with shapeshifters prevalent, time manipulation common, and mind control blatant), focus on the characters' reactions to the ever-changing world. The "meaningful" consequences would all be internal; readers may not care about the external world, but they would care about how characters deal with that external world. True Art Is Angsty and what can be more angst-worthy than trying to discover truth and achieve some measure of inner peace?
If you need to press the Reset Button continuously (e.g., if your publisher mandates that the franchise continue indefinitely), then maybe it's time to adjust the Sliding Scale of Continuity; perhaps moving toward Broad Strokes or even Negative Continuity. It would disappoint long-time fans who were used to the previous policy, but it's better than taking the reputation hit every time you undo any and all consequences which happened in your story. In fact, if each individual story must exist as its own standalone product (with absolutely no canonical or metaphysical relation to the others), then you guarantee that consequences still matter within that story.
This trope was most common in The '90s, with all kinds of works in all kinds of media pulling it and then not knowing what to do with it afterwards. It's the kind of thing often associated with Comic Books of the era (The Death of Superman and The Clone Saga are often cited), but you also saw it in mainstream films (e.g. Alien: Resurrection, The 6th Day), TV series (e.g. The X-Files) and video games (e.g. Metal Gear Solid). That was also when the trope became particularly associated with clones—works of the era had a tendency to introduce multiple clones; which were so pervasive that no character could tell if anyone was the genuine article—not even the character themself. Time Travel was a close second, because once characters had free rein to start hopping through time, audiences no longer had any assurance that any given plot point would not be RetGoned later by some future (or past) time travel shenanigans.
As we're talking about Plot Twists, spoilers ahoy!
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Sherlock: The show's penchant for elaborate segments taking place inside the titular detective's "mind palace", or simply hallucinations, ended up working against it in the long run, as fans begun to dismiss any aspect of the show they didn't like as not real. Thus, there was belief that the very divisive series finale was a Bait-and-Switch, and many fans began searching for clues of a secret real final episode that would be released later. Naturally, these theories were incorrect.
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This has been done so badly to the Terminator franchise that it could very well be one of the main reasons why Dark Fate flopped at the box office. The series as whole never got around to providing a clear and consistent set of rules for how the Time Travel logistics would work, with each new film repeatedly trying to Retcon the rules which appeared to have been established by the last one. According to Word of God, the series was always supposed to take place in a changeable timeline, as the first film was originally going to conclude with the heroes successfully stopping the birth of Skynet and rewriting history. Unfortunately, budget constraints forced James Cameron to save that spectacular climax for the sequel, with the original instead ending with a Stable Time Loop wherein both John Connor's birth and the rise of Skynet were declared inevitable. So when the second film did show the heroes preventing the rise of Skynet, it made it look like the movies just had inconsistent rules regarding time travel. This was easy to forgive at the time, because the heroes' victory made for an excellent finale, whilst the idea of Kyle and Sarah being destined to conceive humanity's savior made for a great love story—even if those two plot points seemed to contradict one another. So when the third film came along and declared that the rise of Skynet really was inevitable, many fans decried it as an Ass Pull that rendered everything that happened in the previous film pointless. The fifth film then tried to remedy this problem by undoing the events of all four previous movies and soft-rebooting the franchise, but this only made matters worse. So by the time the sixth film tried to bill itself as a direct sequel to the second while also having the war with the machines be spearheaded by a new artificial intelligence called Legion, a lot of fans had become so fatigued by all the retcons that they just didn't care any longer.
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The Stanley Parable intentionally invokes this trope. There are Multiple Endings but any time you reach one, the game resets and you are back at the beginning. This is done to (a) make a philosophical point about the nature of video games, and (b) to de-emphasize the Narrator's "story" to instead focus on the relationship between Stanley and the Narrator. This point is most blatant in the Museum ending, though even without that the point is still there.
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X-Men:
Professor X apparently dies during a battle against Grotesk. Later it's revealed that the Changeling had been masquerading as Professor X at Xavier's request.
Jean Grey a.k.a "Phoenix" apparently kills herself so she can't go Dark Phoenix again at the end of The Dark Phoenix Saga. It later turns out to have been the Phoenix Force impersonating the real Jean Grey. (Sometimes. It gets retconned back and forth all the time.)
X-Men: The Krakoan Age ends up inverting the trope, as mutants have banded together and figured out a way to give themselves Resurrective Immortality. Instead of removing dramatic tension, it adds it; as the franchise explores the full political ramifications of a deathless society (what do you do about villains as brutal as Sabretooth when the death penalty isn't an option?), and gives mutants a Dark Secret that would be disastrous if (or rather when) it were ever to be made public.
Sins of Sinister: This Bat Family Crossover event is set in a Bad Future and it's immediately made clear that it will be wiped away, as villain Mister Sinister has a living Reset Button, his cloned "Moira Engine", which will return the timeline to the point when his latest Moira clone was created. Several key characters are also aware of this. However, it's immediately subverted as Sinister loses the Moira Engine and the timeline continues longer than he expected - which means there's a real risk that one of his rival Godhood Seekers will manage to ascend before it resets, becoming a Dominion entity that exists beyond space and across all timelines. In addition to that, one of those rivals (Mother Righteous) plans to send a thousand years of power and secrets back to her younger self. The future timeline will burn away when the Moira Engine activates but, back in the present, Mother will become a much more significant threat if she succeeds - which she does...
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X-Men: The Krakoan Age ends up inverting the trope, as mutants have banded together and figured out a way to give themselves Resurrective Immortality. Instead of removing dramatic tension, it adds it; as the franchise explores the full political ramifications of a deathless society (what do you do about villains as brutal as Sabretooth when the death penalty isn't an option?), and gives mutants a Dark Secret that would be disastrous if (or rather when) it were ever to be made public.
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Alias introduced cloning in the form of "Project Helix", a process by which identical Doppelgangers of people could be produced. The first double was a one-off character, but the second double was a complete shocker: it was Sydney's best friend, Francie. The double was a very unique twist... at first. Then, they brought back the double-switch when someone cloned Arvin Sloane, again later in season four when it was revealed that the woman Jack killed in Vienna wasn't Irina Derevko, it was a double of her and again in season five when Anna Espinosa became a double of Sydney. It got to the point where a common saying in regards to the show was "they're not dead even if we've seen a body - it's probably a clone".
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Naruto was never very good with this, in part because there were so many ways to fool people with hitherto unseen Ninjutsu. And since these guys are ninjas, they've got all sorts of disguise techniques, including clones. Over the course of the series, so many parties are using clones that some enemies need to be beaten more than twice, and there's a huge Gambit Pileup as the different sides start using clones against each other, so no one knows who's real and who's not.
Several chapters after Kisame's original is believed to have been killed, he's revealed to be alive, and the thing that died was really a clone created by Zetsu. Although that type of clone is pretty weird and unique, it still contradicted pretty much everything previously established about how clones worked in the series. It was pretty clearly an Ass Pull in response to negative fan reaction to his death.
The entire first portion of the battle between Sasuke and Itachi involved both combatants just standing still and staring at each other — it was an illusion battle! The only reason we even have to believe that the real fight even happened is that Zetsu, an unrelated third party, appears sticking out of a wall to tell us that the fight is really happening — one party isn't just fooling the other.
It also lends itself to easy Superdickery. At several points, one guy appears to turn on his teammates and attack them — and he's revealed to be an imposter. At one point, Iruka detects an imposter while disguised as Naruto because the imposter disguised himself as Iruka. And the real Naruto was watching the whole thing. And that's actually a relatively simple case.
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From his review of Injustice: Gods Among Us:
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The King of Fighters: '99, the opening chapter of the NESTS saga, introduced a secret conspiracy to clone Kyo Kusanagi and raise an unstoppable Clone Army. Basically, this is an excuse to replace Kyo with his brooding white-haired "brother", K', followed by a pile of rejected clone caca (and Tetsuo Shima Captain Ersatz) called K9999 in 2001. Zero, the Final Boss of 2000 and a mouthpiece for NESTS (but not really), is revealed to be a clone of the original, who shows up in the next game as a sub-boss and is not too happy about his clone's treacherous ways. Again, this was necessitated by the first Zero (and his "fart" attacks) not going over well with fans, and he was replaced with a more stereotypical (yet admirably loyal) white-haired version. Despite rocky beginnings, the NESTS saga is remembered with morbid affection by fans even as SNK seems content to sweep it (especially the above-mentioned K9999, though they certainly weren't above redesigning him into "Krohnen" for his return in XV to avoid getting sued) under the rug for all time.
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Dragon Ball has been having to deal with this for years, due to the franchise having accumulated such a vast pile of instant solutions. Death is Cheap is taken to extremes, with almost every character having died at least once (by the Buu arc of Z, Piccolo is able to suggest that Super Buu kill everyone on Earth because it has no meaning), and there are countless plot devices that allow tension to be instantly dissolved, such as the immediate healing abilities of the senzu beans or the ability to immediately pack in training in the Hyperbolic Time Chamber. Additionally, despite the series being the Trope Codifier for Power Levels, its own powerscaling is notoriously wonky, with characters able to jump up to absurd levels of strength with even the barest amount of training and even relatively weak characters boasting planet-busting power.
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The Adventures of Dr. McNinja cleverly avoids this problem by having all of the cheap clones of Doc that Franz Rayner commissions be flawed and eventually disintegrate. However, there's one original clone left over, raising the stakes on the Like You Would Really Do It cliffhangers that the author frequently employs.
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Sins of Sinister: This Bat Family Crossover event is set in a Bad Future and it's immediately made clear that it will be wiped away, as villain Mister Sinister has a living Reset Button, his cloned "Moira Engine", which will return the timeline to the point when his latest Moira clone was created. Several key characters are also aware of this. However, it's immediately subverted as Sinister loses the Moira Engine and the timeline continues longer than he expected - which means there's a real risk that one of his rival Godhood Seekers will manage to ascend before it resets, becoming a Dominion entity that exists beyond space and across all timelines. In addition to that, one of those rivals (Mother Righteous) plans to send a thousand years of power and secrets back to her younger self. The future timeline will burn away when the Moira Engine activates but, back in the present, Mother will become a much more significant threat if she succeeds - which she does...
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Misfits started to suffer from this in the second season, as Curtis has the ability to rewind time if he feels enough guilt towards something that has happened, giving him a chance to Set Right What Once Went Wrong. So when the Misfits Discard and Draw new powers during the Christmas Episode season finale, the show explicitly removes this power from play.
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The second Clone Saga, written in The '90s, was a response to Knightfall, in which Batman was knocked out of commission and replaced with Azrael, a very different character. Seeking their own version of a Legacy Character, the Marvel writers decided to bring back the clones — but the marketing people wanted to stretch out what was originally a six-month plot to last several years. That led the writers to bring back the clone Gwen (alive), the clone Spider-Man (dead, but alive now because we say so), and the Jackal (dead, but cloned). They also added a menagerie of new clones, including two Scarlet Spiders named Ben and Kaine. This crossover event, spanning across four titles and countless mini-series, accomplished a whole lot of nothing. Nobody knew what was going on, nobody knew who was who, and unlike the "original" Clone Saga, the ending was ambiguous. Early on, hints were dropped that the Spidey the comics had been following for the last 20 years was actually a clone, and that Ben Reilly was actually the original Peter Parker who he'd unknowingly replaced at the end of the original Clone Saga. As the saga got dragged out far beyond the original six-month plan, "proof" kept being brought out and then debunked that one or the other was the true Peter Parker. As the Clone Saga ended, it was leaning toward Ben as the original, and thus Peter retired from being Spider-Man and let Ben take up the mantle of Spider-Man. It wasn't until several years later that it was proven once and for all that Ben was the clone and Peter the original after all, with Ben dying and Peter returning to being Spidey. Most of the clones died, but two (Gwen and Jackal) came back again for Spider-Island. Kaine is still running around doing nothing of particular note.
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The X-Files had a few, that due to alien involvement usually had green blood. Most notable character with plenty of clones was Mulder's sister Samantha.
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This trope is one of Yahtzee's main criticisms of Mortal Kombat—despite the series' trademark high-impact violence, the actual stories suffer from a general lack of stakes and/or weight due to the overabundance of retcons, continuity reboots, and the ease with which characters can be brought from the dead, etc.
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Cradle Series:
Word of God is that this is the reason for the way The Multiverse is set up. The Way is vast, but finite; any story could take place in the Shared Universe, but not every story. The specific example given was that comics can have it where there's a world where everything is the same except your favorite character didn't die. That's not the case here, as each Iteration is vastly different. Even the word "Iteration" is mostly just a reference to the in-universe theory that they're all iterations of an original world, not a provable fact. Therefore, there have to be real stakes and you can't just swap a few timelines if something happens that you don't like.
Likewise, while the Abidan have the power to reverse time and revive the dead (especially Suriel the Phoenix, the primary Abidan viewpoint character), doing this too much risks altering Fate and causing corruption. The series starts with Suriel reversing time so that Lindon was never killed and his home never destroyed, but only because a different outsider had already altered Fate by doing those things in the first place. If he dies again, she can't and won't do anything about it.
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Jean Grey a.k.a "Phoenix" apparently kills herself so she can't go Dark Phoenix again at the end of The Dark Phoenix Saga. It later turns out to have been the Phoenix Force impersonating the real Jean Grey. (Sometimes. It gets retconned back and forth all the time.)
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Gargoyles' creator Greg Weisman tells in 'Ask Greg' of how his children thought Elisa was acting bad in the episode "Protection" because it was a clone, given that an earlier episode had introduced a clone of Goliath. (She was actually pretending to be a Dirty Cop to fool a mob boss.)
At least in the show itself they avoid creating fan confusion by having each clone be a Palette Swap of the original instead of an exact physical match.
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Averted in Transformers: Prime; one first-season episode introduces the villain Makeshift, who could perfectly imitate any other Transformer. He didn't even need to see his victim to do it! The writers then realized that they had created a character who posed far too much of a threat to the heroes and who would dominate the story going forward if allowed to survive, and so they killed him off at the end of his introductory episode.
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The comic later backs up its comments by actually taking advantage of the existence of shapeshifters: In the strips corresponding to A New Hope, the Harrison Ford character steals the "Han Solo" identity from an NPC he kills (the movie's Greedo). He's allowed to get away with it in front of Jabba - for now - because the GM establishes that the original Han was a shapeshifter, and Jabba assumes he's talking to the original in a human form.
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Thanos, the Big Bad in the Marvel Universe, has clones called Thanosi. Thanos's creator Jim Starlin introduced them in Infinity Abyss to explain away any defeats or Out of Character behaviour that Thanos might suffer (which, purely coincidentally, are almost always written by writers other than Starlin). Starlin has even gone so far as to say that not even omnipotent cosmic observer the Watcher can tell the difference between a Thanosi and the real Thanos.
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A slight variation on the trope has begun to appear in A Song of Ice and Fire with the Faceless Men, an order of assassins who can perfectly imitate just about anyone. This has lead to a lot of fan speculation; the only Faceless Man we've really been able to track is Jaqen H'ghar, who seems to have become an alchemist before becoming Pate as of ADWD. Theories now abound as to who might be a Faceless Man, with contenders including Syrio Forel (who may have become Jaqen H'ghar, The Kindly Man, or Ser Meryn Trant after his alleged death), Varys (explaining his exceptional talent for disguise), the guy who was killed at the Sept of Baelor at the end of the first book (meaning Ned Stark might still be alive...), the Brienne that showed up at the end of ADWD, and many, many, many more.
Some of those possibilities are, however, not feasible (however awesome they'd be). The Faceless Men may use something akin to glamour, but it requires a certain key ingredient: a corpse to steal the face and identity of. Also, they will look like the corpse of the person, not the person when they were alive: given how some people can radically change upon death, it's not quite as clone-like as you might think. At best, it's a form of really sophisticated Dead Person Impersonation or Kill and Replace. Even if, as in the case of Pate "the pig boy", they go for as fresh a corpse as possible of somebody they've been tailing for a while, they'll still not quite be right to look at, if you knew the person well before they died. (Faceless Men seem to target those who are foreigners, strangers, generally undervalued or who were always on the periphery of the place they're in — yet, with valid enough reasons for access. In short, people other people don't get that close to, in the main.)
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Later in A New Hope, we discover a rebel pilot who was referred to as Wedge Antilles in the Star Wars movies, and played by Colin Higgins. But Higgins was later replaced by Denis Lawson, resulting in Wedge having a different face in the assault on the Death Star. Darths & Droids plays with it, arguing that Wedge is a Shapeshifter too, which serves the plot for it leads Luke to suspect that he is the traitor who revealed to the Empire the location of the rebel base during the Battle of Yavin and almost the whole The Empire Strikes Back story arc. He was not.
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Blue Drop: The Emul Force allows the user to project their thoughts, creating living sculptures. It's used as a decoy countless times, and every major character death gets undone this way.
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Subverted in Avengers: Endgame. Doctor Strange introduced multiverse theory into the MCU, and while the heroes are indeed able to use time-travel, Banner explicitly clarifies that they cannot change their present by altering the past, as any changes made will only create branching universes which have no effect on their own. This in turn means that, while the heroes could theoretically bring Tony Stark or Natasha Romanoff back from the dead—as ends up being the case with 2014 Gamora—they would only be alternate universe counterparts who would in turn have to leave their old universe(s) behind. Additionally, it's established in Infinity War that the Endgame universe is the only one of 14 million in which half of all life (including the heroes) don't all get killed by Thanos' finger-snap, thus helping to prevent them becoming disposable in the minds of the audience.
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Metal Gear Solid and Metal Gear Solid 2 had far-reaching consequences for the franchise. In an expository cutscene, Snake retcons the ending of Metal Gear 2 by revealing Big Boss was actually his father; the antagonist of the game, Liquid Snake, clarifies that Big Boss was his genetic template and that he and Liquid are both copies of him. MGS2 introduced a third clone survivor, Solidus Snake, who was considered to be the best of the lot despite suffering from rapid aging. The government mothballed the project after Liquid Snake attempted a world takeover by planting Big Boss' frozen cells into a "Genome Army" of sorts. Naturally, this led to quite a few accusations of creating a Kudzu Plot for its own sake.
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Spider-Man: The series has done so much with clones, it's hard to tell which one's the original Spider-Man anymore. There's technically two whole "Clone Sagas"!
The original Clone Saga, printed in The '70s, took place immediately after Spidey couldn't save Gwen. While it was a powerful story, Stan Lee was worried that smaller kids wouldn't be able to handle a character being Killed Off for Real, so he told Gerry Conway to find a way to bring her back. Conway was reluctant, as by then Peter had moved on and was in a relationship with Mary Jane. He used the opportunity to make a story where Peter has to grapple with his feelings of loss and grief, and Gwen has to come to terms with her old boyfriend having moved on and become a different person. That story was delivered with an intended one-shot villain, the Jackal, making clones of both Gwen and Peter, and after some Clone Angst, the real Peter figures out he's the real deal because he's the only one who's in love with MJ.
The second Clone Saga, written in The '90s, was a response to Knightfall, in which Batman was knocked out of commission and replaced with Azrael, a very different character. Seeking their own version of a Legacy Character, the Marvel writers decided to bring back the clones — but the marketing people wanted to stretch out what was originally a six-month plot to last several years. That led the writers to bring back the clone Gwen (alive), the clone Spider-Man (dead, but alive now because we say so), and the Jackal (dead, but cloned). They also added a menagerie of new clones, including two Scarlet Spiders named Ben and Kaine. This crossover event, spanning across four titles and countless mini-series, accomplished a whole lot of nothing. Nobody knew what was going on, nobody knew who was who, and unlike the "original" Clone Saga, the ending was ambiguous. Early on, hints were dropped that the Spidey the comics had been following for the last 20 years was actually a clone, and that Ben Reilly was actually the original Peter Parker who he'd unknowingly replaced at the end of the original Clone Saga. As the saga got dragged out far beyond the original six-month plan, "proof" kept being brought out and then debunked that one or the other was the true Peter Parker. As the Clone Saga ended, it was leaning toward Ben as the original, and thus Peter retired from being Spider-Man and let Ben take up the mantle of Spider-Man. It wasn't until several years later that it was proven once and for all that Ben was the clone and Peter the original after all, with Ben dying and Peter returning to being Spidey. Most of the clones died, but two (Gwen and Jackal) came back again for Spider-Island. Kaine is still running around doing nothing of particular note.
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Blackest Night was an attempt to avert this, as DC claimed it closed the door to future resurrections. It didn't close the door to reboots, though, and the rebooted New 52 brought with it a few characters who came back to life without explanation.
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El Goonish Shive: The only magic that is explicitly impossible (instead of merely out of reach of a particular mage) is time travel. There is some pseudo-time travel with alternate universes that seem ahead or behind other timelines, but they are actually entirely different universes that just appear similar. This trope is the stated reason why; all the drama would drain out of the story if the characters could just hit the Reset Button when something bad happens.
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Averted for the most part in The Punisher since his gimmick is that he kills criminals, after all. That said, some of his villains have been known to come back from time to time, although usually it's a case of imposters (such as Ma Gnucci, actually women who'd agreed to undergo plastic surgery and quadruple amputations), luck (Barracuda being tossed to sharks after they'd eaten a boatful of Corrupt Corporate Executives means they weren't hungry enough to eat him), weird science (despite being reduced to a severed head, the Russian came back with a bio-engineered body that for some reason also gave him breasts the size of beach balls), or just won't die (Deadpool, Wolverine...).
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My Little Pony: Friendship Is Magic:
The show inadvertently did this with the introduction of changelings in the second season finale. Naturally, it caused an explosion of "X is secretly a changeling" type stories in the fandom. A positive side of it is it also helped explain away "clones" in scenes of episodes, that is where the animators reused models in crowds to save time resulting in scenes where as many as six of the same character would be visible — fans (and even the staff) have joked on more than one occasion that said "clones" are actually changeling spies and definitely not the animators cutting corners *wink wink*.
The season 3 episode "Too Many Pinkie Pies" was about Pinkie discovering a magical pond that allowed her to create (extremely one-dimensional) clones of herself. This time around, the implications were addressed, as the cast is shown blocking up the pool at the end of the episode so that there won't be any more clones. And then a later episode undid that by showing another Pinkie Pie in the background who actually reacts to Pinkie Pie bringing up the Mirror Pool clones, revealing at least one of them survived and escaped...
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Secret Invasion: Skrulls did it. To the entire Marvelverse. Lampshaded when Spidey complains that he had clones way before everyone else was getting replaced by Skrulls.
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In one Astro City story, a defense lawyer gets a gangster acquitted of a murder charge by invoking this trope, citing incidents involving evil twins from parallel universes and shapeshifting supervillains. (The lawyer making the argument is Genre Savvy enough to realise that this argument will only work once - it's going to set a precedent that's going to lead to changes in the law in order to prevent it being used as one, and the epilogue to the story notes that this is exactly what happens.)
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Lampshaded in Star Wars Legends with Dark Empire. Basically every time Luke kills a Palpatine clone, he transfers his soul to another clone. Luke pretends to go over to the Dark Side to try and stop him and ends up turning for real.
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Doctor Doom can always come back, because any time he appears to have been defeated (or been responsible for anything the fans don't want to acknowledge), it turns out it was Actually a Doombot. It's so overused that it's long been lampshaded, with fans semi-jokingly claiming that the real Dr. Doom has never actually appeared in any Marvel comic, or even that there is no real Dr. Doom to begin with. Even per Word of God, the only time Doom was ever actually defeated was by Squirrel Girl — and he'll Never Live It Down.
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Zero Punctuation:
This trope is one of Yahtzee's main criticisms of Mortal Kombat—despite the series' trademark high-impact violence, the actual stories suffer from a general lack of stakes and/or weight due to the overabundance of retcons, continuity reboots, and the ease with which characters can be brought from the dead, etc.
From his review of Injustice: Gods Among Us:
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The following is a list of statements referring to the current page from other pages.

 Opening a Can of Clones
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Death Tropes
 Opening a Can of Clones
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Our Clones Are Identical
 Opening a Can of Clones
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Unexpected Reactions to This Index
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Opening a Can of Clones
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