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- One Piece's great prison Impel Down serves as this, as well as being a Hellhole Prison. It holds particularly notorious and dangerous criminals, with 5 different levels of hellish punishments. Meanwhile the secret level 6 qualifies more as a Tailor-Made Prison.
- In Kenichi: The Mightiest Disciple, whenever one of the obscenely powerful martial artists of YAMI are defeated and incarcerated, they're taken to the prison "Big Lock" to serve sentences. However, this is subverted into a Cardboard Prison when the guards eventually realize that the prisoners could easily escape any time they want, but stay put as a matter of honor in having lost their fights. Once YAMI requires their services again, they break right out.
- In Tokyo Ghoul, those Ghouls that aren't outright killed are sent to Kokuria, a special prison in the 23rd Ward. Prisoners are housed according to their threat ranking, and used as informants or for research materials. The walls are made from a special metal (created by combining steel with melted down Ghoul corpses) and a gas that weakens them is pumped into the air to keep them from using their full strength.
- The DC Universe:
- Belle Reve Penitentiary in Louisiana is used to hold metahuman criminals. It is also the headquarters of Task Force X (AKA the Suicide Squad), which allows prisoners to perform dangerous missions in return for a reduction in their sentences.
- In the 30th century, Takron-Galtos is a prison planet used by the United Planets to hold high risk inmates, such as super criminals.
- Marvel Universe:
- Project: Pegasus has been used to hold (and study) high powered super criminals. It was succeeded by The Vault, which unlike Pegasus (a research facility) was purpose-built as a prison.
- The Prison 42. During the Civil War, a group of heroes led by Iron Man, Mister Fantastic and Yellowjacket created a massive prison in the Negative Zone to house captured non-registering heroes as they waited for their trials.
- Massively Multiplayer Crossover fanfic Blood and Revolution has the Japanese government, and later PrivateMilitaryContractors KaibaCorp, creating prisons for the youkai, both legitimate prisoners and political versions. The original was a The Alcatraz-type destroyed by Kenshin and Aoshi, but they get more high-tech and more effective as the decades go on.
- X-Men Film Series
- X-Men Origins: Wolverine briefly featured a series of holding cells that combine this trope and Tailor-Made Prison. Each cell was made capable of holding their individual mutant occupant.
- X-Men: Apocalypse features Stryker's mutant prison, filled with holding cells that somehow dampen all mutant powers, making it the only reliable place to hold mutants prisoner. It also contains a Tailor-Made Prison cell for Weapon X.
- The Ghostbusters' containment unit holds all the ghosts they capture.
- General Zod and his cronies are banished to the Phantom Zone in the 1978 Superman: The Movie. The Phantom Zone is portrayed as an interdimensional wasteland with no hope of escape. Unless, of course, someone therein is needed by the plot, in which case, the Phantom Zone is a horrible vacation spot.
- In Men in Black 3 there's a prison for alien criminals on the moon. The guards have futuristic technology, and the fact that escape means exposure to vacuum also helps.
- Azkaban in the Harry Potter universe is a prison for evil wizards, guarded by the soul-sucking dementors.
- In Myth-ing Persons, Aahz is arrested and imprisoned in a city of vampires. Because a normal jail cell can't hold a vampire, he's placed inside the mouth of an animated dragon-head statue, which can swallow a prisoner who tries to break free or inhale them if they turn into mist.
- Kholomi in Labyrinths of Echo is a prison for mages where magic just doesn't work.
- The Divine Comedy's Ironic Hell features horrid weather, cliffs, monsters, demons, and a doorway marked "Abandon all hope, ye who enter here."
- The protagonists of The Flash (2014) stored captured metahumans in a failed particle accelerator re-purposed to be a prison. In Season 2, once the existence of metahumans becomes common knowledge, the ordinary Iron Heights prison is refitted to be able to handle metahuman prisoners. We're never shown how it works, though. Presumably, though, Cisco is consulted on each prisoner. The cells in the particle accelerator remain, though, and are used twice to temporarily hold people (Harry from Earth 2 and the original Eobard Thawne). Additionally, Zoom holds his special prisoners in small transparent cells that only he can enter by vibrating his body. Barry is able to escape it by copying Zoom's trick.
- In the crossover Supergirl episode, Barry helps the National City justice department do the same to their prison, allowing it to contain individuals with superpowers, as well as to be afforded the same rights of due process as everyone else.
- Tartarus of Classical Mythology, where the souls of the worst of humanity are tormented for eternity along with the monsters that have been banished there.
- Champions has Stronghold, a prison specifically designed to hold super-powered criminals. Exceptionally powerful inmates are kept in Tailor-Made Prison cells.
- The Spellhold, a prison designed specifically to hold rogue mages, in Forgotten Realms. It is also featured prominently in Baldur's Gate II: Shadows of Amn.
- The New World of Darkness has the Lansing Facility, an "ultramax" prison the Vanguard Serial Crimes Unit uses to store slashers who are too dangerous to be brought to trial.
- World of Warcraft:
- The Arcatraz is being used by the Naaru as a prison for some of the most dangerous entities in the universe.
- The Violet Hold is the prison of Dalaran and is designed to hold beings with magical abilities. As of Legion, it's had major breakouts twice, and Lt. Sinclari thinks it's about time they found someplace else to keep these prisoners.
- In Batman: Arkham Asylum, Arkham had special prisons for the super-powered individuals. Poison Ivy, for example, was kept in a reinforced greenhouse.
- Star Wars: The Old Republic: Belsavis, an entire planet used by the Republic as a prison for the kinds of convicts and POWs that can't be kept in regular jail cells. The most slippery escape artist, the most brutal mass murderers, species with abilities that can't be contained, and all of it built on the ruins of an ancient prison built by the Rakata for a race they were terrified of. And that's not even the planet's true purpose.
- Dragon Age:
- The Aeonar is a prison mostly reserved for convicted mages. What distinguishes it from a normal prison is that the veil (the incorporeal barrier between the physical world and the Fade) is damaged due to a brutal massacre of Tevinter mages that took place there several centuries prior, allowing spirits and demons to easily pass through. This makes it a particularly dangerous and hostile environment for mages, who are connected to the Fade and thus are in constant danger of possession by spirits and demons (the latter of which are technically just malicious spirits), giving the Chantry ample excuse to routinely execute its prisoners in a world where magic is deeply feared. The location of the prison itself is unknown to everyone except for a small number of Templars (knights enlisted by the Chantry to hunt down hostile mages).
- It's not just mages who are sent there, either - anyone caught conspiring with blood mages or other maleficarum are sent there as well. At the end of the Magi origin in the first game, Lily, a Chantry sister-in-training, is willfully sent there as punishment for being in love with the player character's friend Jowan, who had been practicing blood magic without her knowledge. The prison is essentially used as a brutal test to weed out hostile mages among the Chantry's prisoners simply by waiting and seeing who doesn't get possessed.
- As of the end of Dragon Age II, the Aeonar is empty with no sign of violence or struggle after the start of the Mage-Templar war.
- The SCP Foundation has a lot of Tailor Made Prisons, but the foundation also has standard cells if the SCP doesn't require any special containment procedures yet risks breaking the Masquerade if it is discovered.
- In Worm, the Birdcage was specifically designed to be proof against escape even by the most powerful parahumans.
- The unnamed prison within Hell in Void Domain. Designed to hold demons. Permanently if need be.
- The Citadel from Star Wars: The Clone Wars was a prison built by the Republic to contain Dark Jedi and other Force-using criminals. The Separatists found that it's perfectly capable of holding good Jedi.
- There were several prisons for benders in Avatar: The Last Airbender, built by the Fire Nation. They were built with precautions regarding the element the inmates were capable of bending: for example, a prison designed to hold earthbenders was built from iron over water, with nary a piece of earth in sight.
- The Alliance in Roswell Conspiracies: Aliens, Myths and Legends has a prison facility for all the various alien they've arrested, many of whom have special abilities.
- The Avengers: Earth's Mightiest Heroes!:
- This cartoon has The Raft, a prison with three layers of security consisting of: all robot guards (no hostages), Power Nullifiers and having the whole prison shrunk to 1/60th scale, so escapees are still small.
- Later on a second prison was built in the negative zone. Here, escape means you end up in the middle of (breathable) outer space.
- Young Justice featured Belle Reve as a sort of prison for supervillains, where the inmates wear collars that inhibit their powers. The compound itself has extremely tight security, including walls not even Superman himself could break through.
- Season One of Loonatics Unleashed housed super-powered criminals such as Mallory Mastermind and the Sagittarius Stomper in the Acmetropolis Prison, miles below ground in a bedrock bunker. Season Two moved many of these criminals to a prison satellite in orbit, adding Otto the Odd and Massive to the inmate roster.
- SilverHawks has the Penal Planet (which actually looks to be a manmade space station). Since most of the escaped inmates that make up the show's Rogues Gallery are powerful enough to require a team of cyborg lawmen to have any hope of recapturing them, calling it a supervillain prison seems reasonable.
- Adventure Time has the Crystal Citadel, a prison for people guilty of the most terrible "cosmic crimes". It's a gigantic six-pointed crystal in an inaccessible Pocket Dimension, watched by colossal Crystal Guardians, where the inmates are entombed in Crystal Prisons. This doesn't slow down the Lich in the slightest when he comes to recruit the inmates.