The prisoner is of noble blood, royalty or otherwise of very high social rank, high enough to be able to claim supreme power;
His imprisonment — quite possibly his very existence or the very fact that he is alive — is a secret hidden from most the guards and/or the people at large
Releasing the prisoner would put the overlord's reign (or plans to reign) in jeopardy
Contrast Hidden Backup Prince, who is a similarly hidden rightful heir, but for protection from their enemies.
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Anime and Manga
This is what the king of the Yellow Kingdom does to his son Len in a non-canon, Vocaloid focused manga adaptation of mothy's "Servant of Evil" upon hearing the murdered fortuneteller's prophecy that the child born with the birthmark shaped like a splatter of blood will bring ruin to his kingdom. The king declares that Len's twin sister Rin is the only heir who was born that night and imprisons Len in a tower where he remains alone until Rin discovers him years later. Justified in that it's made explicit that killing the prophesied child will also bring ruin to the kingdom.
In Marvel's G.I. Joe comic, Crimson GuardsmanFred VII kills the original COBRA Commander and takes his place, concealing his own identity with the mask of CC's battle armour. The Commander turns out to be Not Quite Dead and returns the favour.
In The Warlord, Travis Morgan is captured and imprisoned by Deimos while an Identical Stranger usurps his position as Warlord of Skartaris. An iron mask is locked over Morgan's head to prevent his gaolers learning his true identity.
In the Touhou doujin The Silence of the Rabbits, it turns out that Eirin was incapacitated and replaced by a clone she created to manage her other major creations, but who went very evil. Eirin is a Hourai Immortal and cannot be killed, so the clone had her imprisoned in a People Jar while she spent much of her time as "Eirin" trying to formulate a poison that would kill the original. The clone lived in constant fear of the original Eirin, due largely to the fact that she was designed using the template for the Udonge clones and cannot even hope to match the original in power.
The Man In the Iron Mask has had several adaptions. Richard Chamberlain starred in one where the older twin son had been spirited away, for leverage to make the younger one a puppet king, so the younger one was not, in fact, responsible. But he found out and ordered his brother imprisoned with the mask so no one could use it. The older one was rescued and managed to confuse the younger's flunkies so that his brother was sent off for the same fate. The younger brother was afraid that their being twins meant there might be some connection, so that killing him would be dangerous.
He also thought it would be Tempting Fate to commit regicide, especially of someone who looked just like you.
Le Masque de fer (1962) is a French swashbuckling film. A lighthearted take on the novel, it stars Jean Marais as an old and hammy D'Artagnan.
The 1998 version starring Leonardo DiCaprio as the king (Louis) and twin brother (Phillipe). The movie has the switch between the Evil Twin and Good Twin succeed. Was notable for massive Adaptation Distillation: Louis being more evil than depicted in the novel, and the twist that D'Artagnan was the real father to the twins. This was also DiCaprio's follow-up movie to Titanic during which legions of fangirls were still swarming to the earlier film in theaters: Iron Mask took second place.
In Astérix & Obelix Take On Caesar, Julius Caesar is locked in an iron mask and thrown into a dungeon by the traitorous Detritus.
In Snow White & the Huntsman, Snow is kept alive and imprisoned after Ravenna takes over the kingdom, with no explanation as to why.
King Candy from Wreck-It Ralph usurped the throne of Princess Vanellope von Schweetz by replacing his code with hers. He couldn't out right delete her code, so he turned her into a glitch, leaving her as a prisoner in her own game. On top of that, King Candy locked up the memories of everyone in the game, including Vanellope herself, and developed a Fantastic Racism against her in order to keep her from racing, as her crossing the finish line would cause the game to reset, restoring her rightful place on the throne, and exposing Candy's con.
Subverted in the Sword of Truth; part of the enchantments on the Rahl bloodline make that an unfortunate necessity. Any Rahl who isn't an absurdly powerful wizard is actually a "Pristinely Ungifted" whose propagation threatens the existence of the world. That's not to say that all Rahls kill their children so as to save the rest of their world. Richard runs into most of the survivors over his adventures, with various levels of emotional scarring and insanity, possibly deconstructing this trope by showing what those behind the iron masks would actually be like growing up in their father's country.
Drefan Rahl thinks he's this, but turns out to be delusional and possibly possessed.
Solzhenitsyn's The First Circle set in a Soviet-era "special prison" features a prisoner kept in isolation and referred to by the other prisoners as "the man in the iron mask", although his actual identity is generally known
In The Vicomte De Bragelonne by Alexandre Dumaspère (Trope Namer), King Louis XIV has a twin brother who is kept in the Bastille — by their mother, the dowager queen — to avoid the possibility that he might usurp the throne. To make sure that the guards do not get the wrong idea, the man is placed in a secure part of the prison and forced to wear an iron mask to conceal his identity. This is based on accounts of a real prisoner in the Bastille (among other prisons) forced to wear a mask. His identity was never revealed. This also subverts expectations as the attempt fails, unlike in all its myriad adaptions
Kidnapping the rightful heir was an act of desperation, as the original plan -drug him and make it look as if he were too drunk to be crowned- suffered a Spanner in the Works in the form of a distant relative of the royal family who resembled the heir closely enough to pass as the intended King in the short term. The would-be usurper would have had his brother killed immediately, but that would have made it impossible to depose the ringer without incriminating himself. For the stand-in King's part, acting to rescue the real King would have revealed himself as an imposter, so the situation became a Mexican Standoff.
Parodied in the Discworld novel The Truth, which involves a plot to dethrone Lord Vetinari by framing him for a crime using a man who looks just like him. After the plot is thwarted, William De Worde asks Lord Vetinari if he's giving his look-alike this treatment. Vetinari responds that the man is, in fact, alive and now employed by the Guild of Actors, appearing as Vetinari in stage productions and children's parties. William de Worde theorizes that he might occasionally be used as a stand-in for Lord Vetinari when the real one is unavailable for some boring task or posing for an oil painting, but Vetinari just answers that with a characteristic blank look.
On the other hand, for which of the two is being mistaken for the other more dangerous...? Rhetorical question, of course.
The Mage In The Iron Mask (Nobles series). Includes a lampshading of the fact that a Man In The Iron Mask would have to be let out of it once in a while to shave, or he'd suffocate on his own beard.
In Ursula K. Le Guin's A Wizard of Earthsea, Ged meets two people alone on a desert island, barely capable of understanding human speech. In The Tombs of Atuan Tenar explains that they were the last children of a royal line, and the God-Emperor was afraid to kill them, since they had Royal Blood, so he abandoned them there, very young. Subverted in that Ged did not rescue them; in fact, they were terrified at the prospect of leaving their island.
Notably, they were put to sea when they were children and were now at least middle aged. Royal blood clearly included excellent survival instincts, but they were a bit past their "crown by" date. The God-Emperor may have been cautious, but his grip on power was quiet definitely cemented when he had them exiled.
Eye Of The Dragon by Stephen King. In this case it's the Evil Chancellor who engineers the king's imprisonment by framing him with a very public trial, and when he's eventually freed the replacement king (his younger brother) is all too willing to give him back the throne.
In the backstory of the Ravenloft novel Tower of Doom, a nobleman's wife births a hunchbacked child and his undeformed twin. Their father doesn't lock up the malformed baby's face behind a mask, but he does lie about which kid was born first, raising the handsome younger twin as his successor while his blighted brother, the true heir, is confined to the titular bell tower.
Thenceforward I am Taramis, and Taramis is a nameless prisoner in an unknown dungeon.
Eric does this to Corwin at the end of the first book in Roger Zelazny's The Chronicles of Amber. Somewhat subverted—it is later revealed that this was done as much to protect Corwin as to keep him off the throne.
King Jakoven in Patricia Briggs' Hurog series built the Asylum specifically to lock up his brother Kellen, having been warned in a prophecy that it would be a very bad idea to kill his brother. While it's common knowledge that he's in there, most of the common people seem to have bought the idea that he's genuinely nuts, rather than unjustly imprisoned.
In one alternate-universe in Legend of the Seeker, Richard does this fairly stupidly, though in a rather unusual fashion. Unsurprisingly, it backfires. Turns out, leaving your omnipotence-macguffin out in the open, unstoppable though it may be, is a bad idea.
In the second BIONICLE movie, Lhikan gets this treatment, down to the mask. Weird but funny in hindsight, because most characters wear masks anyway. The character in question actually complied with the treatment to be able to train three of the Toa Metru. It turns out he could have escaped at any time.
Mata Nui by Makuta, though that one turns out to be significantly more complicated.
The real Turaga Duma, by Makuta.
The Toa Hordika could be considered a version of this, though Roodaka tried to execute them by pushing them off a skyscraper.
In another LEGO line, Knights' Kingdom, Lord Vladek usurped the throne and, rather than killing King Mathias due to the threat he posed to Vladek's rule, simply had him locked up in the Castle of Morcia's dungeons instead. Of course, this allowed La Résistance to rescue Mathias, learn of Vladek's true intentions, and ultimately restore the rightful king to the throne.
In Ever After High, Headmaster Grimm's brother Giles is stowed away in the basement of the school. According to the trailer, he's actually trapped down there, and considering the Headmaster's antagonism toward the Rebels before they even do anything, that wouldn't be surprising.
In Arcanum: Of Steamworks & Magick Obscura, while on prison island, the player can stumble upon an old man, who turns out to be thought-to-be-dead rightful king of kingdom of Cumbria. Inevitably, player can help him regain the throne, and inevitably, under his command the kingdom thrives. This is, however, due to his willingness to commence reforms and accept technology (which, by the way, was the reason why he was couped out of power by his technology hating brother), not some kind of magical property of Royal Blood.
Appears in Lunar: The Silver Star. Lemia had her memory wiped by an enchanted mask and is locked away in the dungeon while the usurper takes her place. The cast doesn't realise who she is upon finding her, and free her mainly out of pity and disgust at her... less-than-pleasant condition.
A subversion of this appears in the Kingdom Hearts series, with the character Diz. in reality Ansem the Wise, his kingdom and his very name are taken by his apprentice, Xehanort, whose Heartless and Nobody are the main antagonists of Kingdom Hearts I and II separately. When he escaped from his prison, he decided to fulfill the disguised-face bit himself, with at least one instance of him used magic to impersonate the guy impersonating him.
Because he's technically noble (a knight), Final Fantasy XII's Basch fon Ronsenberg (of Dalmasca) counts. His twin brother put him in prison after he (the twin) framed Basch for the murder of the king of Dalmasca years earlier. The public at large assumed him dead, though instead he's in chains at the bottom of the world's most infamous prison-fortress. He goes on to be freed by Vaan, Balthier, and Fran, eventually joining them permanently in order to safeguard Princess Ashe.
In Mileena's ending in Mortal Kombat Armageddon (non-canon, like pretty much all the others), she will do this to Kitana after Blaze's scattered essence causes them to exchange looks (i.e. Mileena gets a normal face, Kitana ends up looking like a Tarkatan). As a result, Mileena becomes free to drive Edenia to destruction without any hitch, while Kitana will Go Mad from the Isolation.
Used in The Legend of Korra with Amon keeping Tarrlok imprisoned on Air Temple Island due to the two of them being brothers. In true trope form, it ultimately proves to be Amon's undoing as Korra uses Tarrlok's knowledge of Amon's true past to turn the Equalists against him.
My Little Pony: Friendship Is Magic: Has Princess Cadence, who was imprisoned in some sort of crystal mine while Chrysalis, Queen of the changelings, took her place. Twilight sparkle then gets thrown into the same place and breaks her out.
The legend of the Man in the Iron Mask was based on actual records found from Bastille. There are a lot of theories regarding the Man's identity, but very little information remains of the real events. What has been discovered is that the Iron Mask itself was an exaggeration - the mask was just silk, and the Man probably wore it voluntarily. A fair amount of evidence points to his having been an insignificant figure whose knowledge was dangerous, not he himself. You will not find that in any of the legends.
Aversion: The Ottoman Sultan Mehmet II (the guy who took Constantinople) realized that having siblings around to challenge the throne was not a good thing for the ruler and the kingdom so he not only recommended fratricide, he legalized it (on a royal level) and put together a framework to deal with troublesome siblings. It was only removed during the later periods of the empire and overall, it is generally considered a success (though it had the unfortunate side-effect of making said siblings mentally unstable and paranoid).
Ivan VI Antonovich Romanov, an Emperor of Russia. Crowned when he was one year old, after his great-aunt Empress Anna Ioannovna the Bloody died. Deposed by Elizabeth of Russia, who thought that, as the daughter of Peter the Great, she has a better claim to the throne, one year later. Grew up in prison, understandably strange and lacking in education, but knowing well who he was. One disgruntled, plotting Guards officer in Catherine the Great 's times tried to free Ivan Romanov and reinstate him on the throne. It ended in both Ivan and the guardsman killed.