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Anime and Manga
- In Digimon Adventure Datamon captures Sora and soon afterwards makes a copy of her to use against Etemon thinking Biyomon will fight for him.
- In the Pokémon movie Pokémon: The First Movie, Mewtwo captures the Pokemon of the trainers he lures to his island so that he can clone them all.
- Ranma ˝: Akane Tendou is captured and replaced with a double via Jyusenkyo Spring.
- Tenchi Muyo!: In the "Zero Ryoko" two part mini-arc, Dr. Clay becomes curious about Washuu's interest in Tenchi. So he kidnaps her daughter, Ryoko, then has his android assistant (Zero) take her form and assimilate her memories, in order to spy on Washuu. Clay had intended to dispose of Ryoko immediately, once the replication was complete, but when Zero notes that a portion of Ryoko's memories was missing and couldn't be accessed, it piques his scientific interest again, so he begrudgingly decides to keep her alive.
- Tsubasa Reservoir Chronicle gets considerably darker when it turns out that the Syaoran and Sakura who had been traveling with Fai and Kurogane ended up being clones of the originals, whom Fei Wong Reed had captured sometime previous.
Film - Animated
- In The Princess and the Frog, part of the plot involves Naveen's servant Lawrence passing as him. This is done thanks to a talisman that lets Lawrence look just like Naveen, but needs a drop of Naveen's blood once a day or so to continue working. However, Naveen escapes early in the movie and the bad guys spend some time trying to find him.
- The Swan Princess: Towards the end, Rothbart has Odette locked up as a swan in a dungeon, and turns Brigit into a look-alike of Odette, sending her to trick Prince Derek.
Film - Live-Action
- In G.I. Joe: The Rise of Cobra this was Cobra's plot when they used agents in the President's Secret Service detail to capture him so that Zartan can shape his physical appearance after him and use his name to accuse the Joes of being rogue agents in G.I. Joe: Retaliation.
- Oblivion2013: Jack and Victoria were astronauts on a mission to Titan when Mission Control picked up the Tet and sent them to investigate. They were captured, cloned and then sent back to Earth to take it over. Years after, clones are still used to maintain equipment while the Tet drains the world of water to power itself.
- In the Harry Potter series, Polyjuice Potion can allow one to mimic any person, but it requires a piece of the person, usually a hair. The piece must be recent and taken while the subject is alive, so in order to impersonate them for more than a few hours, it's necessary to keep them captive somewhere. In Goblet of Fire, Barty Crouch Jr. does this with Mad-Eye Moody in order to impersonate him throughout an entire school year.
- In Newsflesh, the reason why President Ryman hasn't been responding to the After the End Times team's calls for help is that his wife and children are being held captive and have been replaced by docile clones for public appearances. All they do is smile and wave.
- Appears in the German SF novel Der Verbannte von Asyth, whose plot revolves largely around aliens replacing important individuals on Earth with masked infiltrators of their own kind. The originals are kept alive at the aliens' hidden base and thus remain conveniently available for questioning.
- Done occasionally on Doctor Who. Specific cases include:
- The Zygons from episodes "Terror of the Zygons" and "The Day of the Doctor" are shapeshifters, but need to keep the original person they're replacing alive so they can have a psychic link with the victim, in order to have access to the original person's body print.
- In the two-parter "The Sontaran Strategem" and "The Poison Sky", Martha Jones is put into some kind of slime vat and a clone is grown from a nearby pod. The clone gradually becomes an independent being and the Doctor is able to talk it into helping him save the day.
- There's a two-parter that examines the ramifications of workers putting their minds into synthetic bodies, called Flesh, for their own safety, when a power surge causes the duplicates to become independent. At the end of "The Almost People", Amy is revealed to have been a Flesh duplicate for a significant part of the series, with her actual body held by the Silence organization in order to take her newborn child and raise it as a Laser Guided Tyke Bomb.
- In the Stargate SG-1 episode "Foothold" the SGC is invaded by an unidentifiednote race of Humanoid Aliens that imprisons its personnel and uses them to create holographic disguises. The prisoners are kept alive to allow the aliens to mimic their normal behavior via technobabble.
- Star Trek: The Next Generation: A group of aliens capture Captain Picard and replace him with a double in the episode "Allegiance". This was part of an experiment to examine the nature of authority, as they were a Hive Mind with no concept of individuality or hierarchy. The real Picard was locked in a cell with three others to see if they could work together to escape; the fake Picard on the Enterprise gives his officers increasingly insane orders to test their loyalty.
- Star Trek: Deep Space Nine:
- In the episode "Whispers", Chief O'Brien is captured and replaced by a clone. The replacement is too perfect of a copy, and has all of O'Brien's memories and emotions, and doesn't know that it's supposed to be working for the captors, and instead disrupts his own scheme when he becomes aware that something is amiss.
- In another episode Martok, the right-hand-man of Klingon Chancellor Gowron, is discovered to be a Changling and killed. Later Worf discovers a Changeling prison camp where the real Martok is being held captive along with other prisoners.
- And while there, he also discovers that the Dominion has had Doctor Bashir in the camp as well, and that he's been there for at least a month or two- which means his impersonator has had that long to wreak all kinds of havoc unsuspected.
- In Ironclaw the druid spell "Steal Guise" allows one to impersonate another, but only so long as the real one is alive. The adventure "The Rescue of Miranda Devoisier" has a side quest where the head of a family is kidnapped and impersonated by a rogue druid using that spell.
- The Demoreans of Timemaster can do a short-term shapeshift without capturing their model first, but for a shift that's expected to last any length of time the model needs to be stuffed in a sleep pod.
- In Chrono Trigger, Yakra captures the Chancellor of Guardia and poses as him mainly to serve as an Obstructive Bureaucrat in his aim to destabilize the kingdom. Four centuries later, his descendant Yakra XIII does the exact same ploy. You can expose and kill him and free the real Chancellor during the Rainbow Shell subquest.
- The plot of Jumper Two revolves around an enigmatic hooded person known as The Boss trying to capture Ogmo, "the ultimate soldier", to create an army of OgmoBots with which he is going to Take Over the World.
- Metal Slug 3: Halfway through the 5th stage, one of the player characters will get kidnapped by the Mars People. Later, as you storm the Martian Mothership, you'll find clones of said character as your enemy; much later, you'll find said character in an aquarium-esque confinement where you have to rescue him/her while clones of said character attack you en masse.
- In one side quest in Pillars of Eternity, a woman asks you to deliver a divorce notice to her husband, who has been acting strangely towards her lately. If you investigate their home, you find out that he has been locked up in the attic for days, while a criminal mage assumed his appearance and used his home as a hub for his drug trade.
- In Saints Row: The Third, The Syndicate captures Oleg Krilov—a giant of a man—and keeps him sedated in their labs to mass-produce clones of him and throw them at the Saints. One mid-game mission sees the Saints infiltrating said labs and freeing Oleg to stop the clone production.
- Batman: The Animated Series: An evil A.I. called HARDAC captures several prominent citizens of Gotham City and replaces them with androids.
- In Futurama episode "I Dated A Robot", Nappster (actually Kidnappster) holds celebrity heads in order to transfer copies of their personalities and appearances onto blank robots (as a parody of the original Nappster website). In this case, the users know they're downloading copies, but not that the originals are being held captive, and painfully shocked whenever a copy is made.
- In the animated The Legend of Zelda, one of Ganon's plots to steal the Triforce of Wisdom was with a magic mirror that created a copy of Zelda and also allowed her to be taken to his realm, where she was tied to a spike in Ganon's chamber, but managed to escape.
- Mega Man: in the episode "Bro Bots", Dr. Wily's latest scheme is to kidnap the newly-elected Governor on election night, and replace him with a robotic duplicate. Megaman, despite having been incapacitated earlier, manages to stop him and save the Governor-Elect.
- Turns out to be what had happened to the real Roy Harper on Young Justice: The real one had gone missing on a mission and had been captured by Cadmus. They sent a clone in his place (and halted his aging) as a Manchurian Agent against the League, whose members were none the wiser until he unwittingly turned against them.