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the original Yu-Gi-Oh has the playable Egyptian GodCards. There are also a number of arch-demonlike/godlike cards out there. Timaeus & company, Exodia, Dark Ruler Ha Des, Dark Creator, the Sacred Beasts, Black Luster Soldier and Chaos Emperor Dragon, Five God Dragon, and the list goes on. Most characters who use these cards do so frivilously; Yugi, being the hero, is likely the only one who at first realizes the potential danger they may pose. (As he says when he wins Sky Dragon Osiris, "I must be very careful with this...") Heck, even Blue Eyes White Dragon had a god-like backstory before the game's Power Creep got the better of it. And there's still its fusion forms, the Blue Eyes Ultimate Dragon (which even after the power creep still has the 5th highest attack power in the game, with all of the stronger cards being ludicrously impractical to use) and the even more powerful Dragon Master Knight.
The spinoff manga Yu-Gi-Oh! R features the Devils, demonic doppelgangers of the God Cards. The second series, Yu-Gi-Oh! GX has the Sacred Beasts, another set of Evil Counterparts of the Egyptian God Cards. To make that even worse, there's even a far stronger monster that's summoned by fusing all three of them. The third series, Yu-Gi-Oh! 5Ds, features two opposing sets of "God Cards" in the form of the eponymous Five Dragons, each wielded by chosen heroes called Signers, and the seven Earthbound Gods, nightmarish monsters of enormous size inspired by the Nazca Lines whose masters, the Dark Signers, came Back from the Dead through a Deal with the Devil.
Trueman took it Up to Eleven in the fourth season of Yu-Gi-Oh! GX, actually summoning two copies of Five God Dragon at once. (Which kind of makes you wonder, just how many people in this reality have access to this card, which is stronger than Obelisk? Even Judai had a copy.) In fact, the method he used was even possible in the real game at the time. (But not anymore, at least currently, because Future Fusion is now illegal.)
In Digimon Tamers, Guilmon's "dark evolution" turns him into Megiddramon, a Dragon who can destroy all of reality. Unlike most examples, Takato could not control him, and he had to come to grips with his own anger at someone who had killed a friend before Guilmon would revert back. In fact, most of the Digimon games have something like this. It's possible to obtain, through evolving cute little In-Training level Digimon, godlike Digimon such as Alphamon and Chaosmon who have unfathomable amounts of power. There's also Goddramon, often translated as Goldramon in English.
In Digimon Savers, awakening and controlling the apocalyptically-powerful demon Belphemon is Kurata's ultimate plot.
Those that go Serial Escalation, the rarely seen "Super Ultimate" or "Ultra" digimon, which include the likes of Daemon Super Ultimate and Chronomon. The latter is the final boss of Digimon World DS, where it can be befriended and trained.
In Narutaru, two characters get control of a shadow dragon of incredibly ridiculous proportions: the Earth itself.
Ash has encountered a couple of trainers with Legendary Pokemon on their teams, such as the Pyramid King Brandon who owned all three of the "lesser" Regis, and the mysterious Tobias, who owned Darkrai, Latios, and possibly others. (He defeated Brandon after the third attempt, but failed to defeat Tobias, although he did put up a far better fight than any of Tobias' other opponents did. While Ash himself has never managed to actually tame a Legendary, he has befriended a lot of them over his career. In fact, Ho-Ohnote First seen at the VERY FIRST EPISODE seems to favor him at times, as it has appeared on many occasions to give him inspiration when he is considering giving up.
If the 10th and 11th movies didn't prove how good Ash is at making friends with actual gods, then the 12th movie will go to show that he's now officially friends with Arceus, itself.
In several storylines it's been treated as an innately bad thing to capture a Legendary Pokemon (in the 2nd movie, for example, capturing the Legendary Birds causes the world's weather to go haywire). But befriending one and getting it to voluntarily join your team? That's always fair game.
The plot engine of the Spirit Animals series. The Four Fallen, the four Great Beasts who died centuries ago to stop the Devourer, have returned as the spirit animals of four eleven-year-old kids. Suddenly, those four become the center of the defense against the new Devourer.
Well, the creator has never really mentioned whether this is correct or not, but it's safe to hazard a guess that Vivipahge, Vaccuthax, Psychodrome, Azavoth, Grenzo, Ziafel, Chimerinsect, and most of the Devilbirds are these for Mortasheen. Caterpucker and most of the "Ultimate Garbage" are this combined with Magikarp Power. There's also the Ultimates, which include Tormanshee, which turns people into a neural network computer with Mind Rape, Mothneaser who is a giant floating pillar of flesh which creates horrible things out of its own blood, as well as using it to puppeteer beings that come into contact with it, Hestermoan who is a horrible Nucklavee looking thing that spreads plague and was; to quote; "engineered by an unknown party as an instrument of genocide against an entire civilization, and so effective that their very name remains unrecoverable", and Necromon, who is the Mortasheen equivalent of Mew who specializes in Karmic Transformations.
Another example is Oovule, which can only be described as a Crystal Dragon Jesus that has brought countless beings back to life, and its considered a Zombie type; the Abnortis, which is a Zombie type and a corrupted clone of Oovule; and two Devilbirds, Astarath the ultimate liar and Mephilas, which can extend your knowledge to the point that you'll become a Straw Nihilist... and no one knows where they come from.
Monsters And Other Childish Things is pretty much based on this concept. Your character (who may be anywhere from 8 to 18 years old depending on the game) has a pet monster that's his or her absolute best friend, and backs the character up in fights against other kids and their monsters. The adult world generally knows about these monsters, but is powerless to stop them - only monsters can really hurt other monsters, and they can tear through people and most earthly materials like tissue paper. Most monsters are some form of Eldritch Abomination to boot.
Magic: The Gathering has tons of creatures that can easily count, most of which are Legendary. One of the most famous examples is Progenitus, with his famous "protection from everything". The flavor text, "The Soul of the World has returned", pretty much say it all.
The game allows you to capture, among other things: The common ancestor of most other Mons and its Super SoldiercloneGone Horribly Rightnote Mew and Mewtwo; a time-traveling avatar of floranote Celebi; the embodiments of the earth, sea, and skynote Groudon, Kyogre, and Rayquaza; the masters of time, space, and antimatter/deathnote Dialga, Palkia, and Giratina; the creators of free will, emotion, and knowledgenote Azelf, Mesprit, and Uxie; the new moon/a living embodiment of nightmares and the crescent moon/living embodiment of dreamsnote Darkrai and Cresselia; another avatar of flora for good measurenote Shaymin; golems of rock, ice, and steelnote Regirock, Regice, and Registeel; elemental birdsnote Articuno, Zapdos, and Moltres and beasts note Suicune, Raikou, and Entei of water, thunder, and fire; twin dragons with enough psychic firepower to stop a tidal wavenote Latios and Latias; a colossal golem that supposedly moved continents and created the aforementioned rock, ice, and steel golemsnote Regigigas; a volcano spiritnote Heatran; a wish granting Fun Size starnote Jirachi; the prince of the seasnote Manaphy and his sonnote Phione; a rainbow phoenix and a draconic bird that can cause storms with a flap of its wingsnote Ho-Oh and Lugia; a shapeshifting alien virus creaturenote Deoxys; and what is outright stated note In the Heart Gold and Soul Silver Dex entries to be the creator of the Pokemon universe itselfnote Arceus.
As of the 5th gen, we get a small critter that is the personification of victory (and possibly a nuke)note Victini, The Three Musketeers and D'artagnannote Cobalion, Terrakion, Virizion, and Keldeo, dragons of Yang, Yin, and Wuji that were originally one entity that may or may not have been an aliennote Reshiram, Zekrom, and Kyurem, the Japanese gods of wind, thunder, and fertilitynote Tornadus, Thundurus, and Landorus, a musenote Meloetta, and a long since extinct insect resurrected from a fossil and cybernetically enhanced by Team Plasma scientists in the hope of creating the ultimate weaponnote Genesect.
With the arrival of Pokémon X and Y, one can now have the avatar of lifenote Xerneas, deathnote Yveltal and ordernote Zygarde.
There are also what are known by the fandom as "pseudo-legendaries", which are standard Pokemon with power well beyond other standard Pokemon and even some of the legendaries; they consist of a friendly-but-extremely-powerful Eastern dragon note Dragonite, an extraordinarily strong and violence-prone kaiju note Tyranitar, a lumbering mech with a supercomputer for a brain note Metagross, a wyvern note Salamence, a desert-dwelling shark/dragon hybrid note Garchomp, a ceaselessly destructive and ravenously hungry flying hydra note Hydreigon, and a slug-dragon hybrid that, while very friendly and good-natured, is still a tour de force in combat note Goodra.
In-game, there's what you call "lesser" legendaries. They are generally the non-cover Pokémon trio like Articuno-Zapdos-Moltres or Cobalion-Terrakion-Virizion. Unlike, say, Mewtwo or Arceus, they aren't restricted and thus fine to use in Battle Frontier, Battle Subway, and Pokémon World Tournament. They're also legitimate Pokémon to use in official tournaments.
Apparently, you can do this because the Pokeballs work as power limiters, allowing you to control them. This is one of the reasons why the big bad of Pokémon Diamond and Pearl wants to control the masters of time and/or space by force, rather than capturing them in Pokéballs.
"You can say whatever you want. A Pokémon, even if it's revered as a deity, is still just a Pokémon."
Mind you, Arceus isn't the monotheistic conception of 'God'. In the most common religions in Japan and Asia, the 'creator' deity that Arceus is based on usually creates the world partly or entirely by accident, and doesn't necessarily control it.
Some Legendaries are allowed in standard tournaments, because some of them aren't built to play competitively. Regigigas, due to its terrible ability (half speed and attack for five turns) is in the same tier as Beedrill.
Made even more evident in HeartGold and SoulSilver, when the player is able to have his/her lead Pokemon walk behind the player. A "second-tier" legendary such as Zapdos looks like nothing out of the ordinary, but try putting Ho-Oh in the lead. It's at least twice the size of a normal Pokemon, and you can't even have it out indoors. Yet the NPCstake no notice of it. And thus Pokémon-amie answers that long lost question - Yveltal is adorable when you try to pet it.
The same with people who judge your Pokemon's potential, name raters or Pokemon Salon workers, since they're scripted to say the same thing, they have no unique reaction when you bring "God" in for a massage. It's kind of a let down actually...
Arceus in particular can only be gained through Wi-Fi events or visiting certain shops on certain dates. Originally Arceus was to be catchable in Generation IV games via an event item but it was Dummied Out and so Arceus became limited through distribution via events only. This becomes somewhat of a Fridge Brilliance because the player technically does not catch Arceus, but rather has its power being "loaned", so to say.
Oddly enough, story-wise, while it seems easy enough for the heroes to tame these creatures, villains aren't so good at it. With the exception of Team Rocket and Team Plasma in their first appearance, the villain team's Evil Planalways involves harnessing the power of a Legendary in some way. It never works. Either the Legendary sides with the hero or lashes out at everything in anger, forcing the hero to battle it in order to calm it. The only villain to have any success taming one in N, if you can even call him a villain. (Maybe these creatures just like children better?)
NetHack lets you tame two of the three Horsemen of the Apocalypse (the player is implied to be War, and outright stated in a comment in the source code). It's a bit tricky, and requires you to hit them with a few Level Drain spells first. You can get the third if you slime him, but then he's permanently transformed and thus not a Horseman anymore.
On the other hand, NetHackGame Mod "SLASH'EM" makes it possible to transform monsters temporarily. Thus, in it you can potentially lead all three of the Horsemen of the Apocalypse around on leashes.
In TOME, you can wield one of the Bonus Bosses as a symbiote if you have a high enough level, and make the other two "join" you by killing them, then using a wish spell to create a loyal companion possessing spirit to revive their bodies. Plotwise, it's not their souls running the bodies, but mechanics-wise it works. Note, one of these characters is the Author Avatar of the programmer.
The Shin Megami Tensei series has several examples over the course of its history. Satan? The Fates? Pretty much every mythological god ever? Sure—you can order them around to your heart's content! Notably, however, the ultimate antagonist in each game can only be defeated and/or destroyed even if your party has previously subdued the opposite-aligned equivalent — not that there would be any point in a capture. Example: in Shin Megami Tensei III: Nocturne, Kagutsuchi sends out Metatron, the Voice of God, to warn you against doing a very bad thing. You do the very bad thing, and Metatron fights you. You defeat the Voice of God, and it becomes just another one of your footsoldiers. Whom you can use against Kagutsuchi himself. And that's just the tip of the iceberg! It's also possible to have LITERAL Olympus Mons, too: the Greek pantheon is well-represented in the series. The game's version of Cerberus is also one of the game's mascots, along with good ol' Jack Frost.
One particular deconstruction of this trope is Devil Survivor; you play as a group of teenagers with Nintendo DS-like portable gaming consoles that can summon demons to attack their enemies — and so can anyone else in the city with the same device. Society quickly begins to break down, since people aren't supposed to have this kind of power without restriction, and the whole area is devastated within a week's time.
In the MMORPG, Shin Megami Tensei IMAGINE, one creature implies that when they allow you ally with them, you gain huge control over them via the device used. This implies that if they don't like you, such as being allowed to die all the time, they still have to serve you because the device controls them directly. She notes:
Fairy: I don't like being told what to do, but when my partner presses that button I just can't help myself.
In the Undead Nightmare expansion pack for Red Dead Redemption, it is possible for John Marston to tame all four of the Horses of the Apocalypse (Death, War, Pestilence, and Famine). All are incredibly fast and have infinite stamina, and Death causes any zombies it touches while sprinting to have their heads explode.
In Dragon Quest Monsters, you can create your own versions of the bosses. Multiples, even. In Joker, it's not difficult (though it is time-consuming) to have an entire party of the final boss by the time you fight him. Additionally, two of the higher-level Monsters in Joker are the Final Bosses of Dragon Quest II and III. The punchline? They're most useful as healers.
The freeware RPG Well of Souls has several unusually powerful creatures available for taming, such as the embodiments of all the world's elemental forces. However, it also averts it, in part—there are some monsters whom you can never, ever tame; usually because they're a higher level than you can ever be, and you must be at least a level higher than a monster to tame it.
World of Warcraft occasionally scratches this with Hunters being able to tame creatures far more exotic than your average bear or turtle. Indeed, a recently added Beast Mastery talent lets Hunters tame several types of animals classified as exotic, including two-headed hounds (one variety looking like a raid boss, one being almost exclusively encountered in a raid dungeon, and, most recently, one that IS a raid boss, and gets to keep it's raid boss level tag) and the infamous Devilsaurs. And then there is the collectors edition bonus, noncombat pet from another Blizzard game.
Perhaps more fitting to the trope, there are some minor god-things (like Arikara or Anzu) that can be used as mounts or hunter pets.
And there are tried and true gods hunters can tame, Loque'Nahak, mate of the snow leopard goddess Har'koa, and three more loa (a cougar, an alligator, and a gorilla) in Stranglethorn Vale as of Cataclysm, the latter of the three don't even need to be beast masters to tame and use.
Gotcha Force also features this, though attempts to mitigate it by having borgs above the Com Mons level require "data crystals" - "A" and "B" for things a bit beefier than the basic set, all the way through "A" through "E" for the most powerful. The problem is that you need one of each letter, so it's common to sit on multiple copies of "B" while you wait for a single "A". Also, the different palettes do not have interchangeable crystals - good luck getting some of those.
In Dwarf Fortress Certain large and potentially quite dangerous creatures can be tamed if captured without killing a dwarf, including dragons (officially bosses). You can KO the Hidden Fun Stuff via cave-ins and stuff them in cages; they aren't tameable without a minor hack, but can be tossed into a pit to be fed with enemy prisoners.
RuneScape has the summoning skill, where a player can keep a series of more dangerous "familiars" that approach Olympus Mon strength as the player levels up.
Scribblenauts lets you summon, and then mind control, Cthulhu. You may then RIDE HIM AROUND. You can also summon God and Death and have them fight each other for your amusement. Really, Scribblenauts is practically built on this kind of power-abusing potential.
It is unclear in Final Fantasy lore exactly who or what the Knights Of the Round are, and even more unclear why exactly they are taking orders from creatures they could kill 10 times over with a single go.
Let us not forget the leader of the Wild Hunt and patrician of all glorious souls, the king of all dragons, either the female side of the Hindu god(dess) of destruction (and currently second or third most worshiped deity, behind the Abrahamic god) or a deity from another pantheon, an embodiment of untamed and destructive nature that had to be imprisoned by a more civilized god, another god of death (named after the Greek deity, portrayed as the Celtic Arawn or Dagda), the Garden of Eden, and a living black hole (that doesn't kill the players). None but perhaps that dragon or the Garden of Eden are as powerful as Knights of the Round, but it's not surprising that the eponymous Unlimiteds from Final Fantasy: Unlimited are described as having power surpassing that of the gods.
In Final Fantasy IX, the summons are treated like the god-like beings they are by the plot, and controlling them is a very big deal.
Tales of Symphonia has Sheena, who can control the eight beings that embody the elements (known ingame as Summon Spirits), along with Origin and Maxwell, both essentially gods, and Corrine, a manmade (not exactly) lesser Summon Spirit.
And its predecessor (chronologically its distant sequel), Tales of Phantasia has Klarth/Claus, who can do the same thing.
Tales of Xillia has Milla, who can control the four great spirits of the elements in battle, what with how she outranks them in the hierarchy of spirits. She loses this ability for most of the game after she gets de-powered by the Lance of Kresnik, but regains it when she rejoins your party late in the game. Jude also briefly has the ability to summon Muzet, who is equal in rank and power to Milla, but he loses the ability after she betrays the party.
In Custom Robo you can acquire the illegal parts for your robo. These parts are said to be so powerful that they actually pose a high chance to cause mental and physical harm to those who use them. Yet, the main character (usually a kid who basically started using Custom Robos a week ago) is fully capable of using them. That includes the parts for the final boss of the Gamecube one, which was bio-mechanical and destroyed most of the Earth and Humanity, save for a single dome.
In Monster Rancher, the Gali species (and, in the first game, the Magic species) are said to be gods in the guise of monsters, with all the attendant power. People and other monsters are awed by them. This, however, is actually a case of Gameplay and Story Segregation, as Galis are no more inherently powerful than any other monster, and still need careful training to achieve their full potential.
The Valsharess in Neverwinter Nights Hordes of the Underdark summoned and bound Mephistopheles. And if you find his True Name you can claim absolute authority over him in the endgame.
Azure Dreams has 15-year-old hero Koh obtain the world's only Shadow-type dragon monster which is supposedly capable of destroying the world. That is not hard to believe, given that its two main abilities are bestowing invulnerability and unleashing an One-Hit Kill on anything...
Long before obtaining The Ultimate Egg, though, Koh trains up a lot of other terrifying monsters - from the lowly Pulunpa up to Golems, Killers and Dragons. Quite a few of these creatures qualify as Olympus Mons themselves.
Became a problem in Disgaea, particularly the second one, where a bug made it possible to capture a level 9999 Nekomata early on, and use her to steamroll the entire rest of the game. Later games fixed this by making it impossible to capture any monster who is higher level than the main protagonist.
Robopon has Golden Sunny, Silver C-Cell, and Scar in the first game, and Nebulus in the second.
By maxing out your Social Links in the Persona series, you're given the ability to fuse and create the "ultimate forms" of that Link's Arcana. For example, by meeting the right conditions in Persona 4 Golden, you can create the end game Izanagi-no-Okami.
The same playthrough also did this to a Pidgeot, of all things. When the starter was accidentally released, the Pidgeot became the only high-leveled Pokémon in the party and carried much of the run by himself. This led to him becoming known as Bird Jesus, Savior and Messiah of Twitch. When a Master Ball was successfully used to capture a legitimate Olumpus Mon: Zapdos, he became widely known (amongother things) as "Bird Jesus 2: Electric Boogaloo".
Since then they've obtained two more legendaries (Mew and Groudon) though not in the usual manner—they were obtained from NPC's in randomized games, whereas in the unmodified game they wouldn't have been anything too special.
Pokemon Digimon Mon Wars: The Digidestined learned the hard way just how powerful Legendary Pokemon are. Originally only the Legendary Pokemon (and Mega Evolved) could have stood up to Ultimate and above leveled digimon, but once the Sealed Evolution had been unlocked, its possible for pokemon to reach such a status.
In one episode of Pinky and the Brain, the Brain actually gave the Earth itself a voice and befriended it. This was possibly the closest he came to truly conquering the world, as he was able to force nations to submit to him, able to drag them under the sea if they didn't comply. Unfortunately for him, he made it angry at him and it wanted to kill him, a very good example of why this trope is so dangerous. When it looked like his only means of survival would be to escape into outer space, Pinky convinced the Earth that it wasn't happy the way it was, and it let Brain reverse the process and return it to an inanimate state.
The Ancient Psychic Tandem War Elephant in Adventure Time reads Finn's mind to determine if he is worthy to command it. He is.
The 626 series of experiments in Lilo & Stitch were created with this trope in mind. Unfortunately for their creator, most fall very short of the mark.