Super Dimension Fortress Macross: To the Zentradi, humans are this. Their first contact with Earth occured while they were chasing an enemy ship (that was reconstructed into the titual space fortress) and they had no idea what humans were or why they attacked them (the crashed ship had a booby trap on it). Humans then frequently act in a manner that the Zentradi find inexplicable and disturbing, usually as a result of cultural pursuits or rashly using technology they don't fully understand. They initially assume that music is some kind of psychological superweapon, and expressions of interpersonal affection to be akin to a literal superpower (which also confuses them when they first see a film and believe the special effects are real).
Bleach: Yhwach was a bolt out of the blue for Ichigo's group and the Gotei 13. Mayuri did actually foresee Yhwach coming as a result of Uryuu Ishida's actions in the Soul Society arc, but when he tried to warn Yamamoto, Yamamoto dismissed Mayuri's concern as paranoid. Had he listened to Mayuri, the Gotei 13 would have had more than 17 months preparation time instead of being caught completely unaware and unprepared by a quincy army they didn't even know existed. It's also very heavily implied that Urahara, Isshin and Ryuuken have been fully aware of Yhwach's activities for at least nine years and possibly longer but they have kept the knowledge within their tight circle which also left both Ichigo's group and the Gotei 13 completely unaware and unprepared. However, this is implied to be because Urahara's group have their own plans rather than burying their head in the sand as Yamamoto did.
The Apostles from Berserk are far more powerful than normal humans, and there are several Apostles above even them. The Five Godhands and the Kushan Emperor are terrifyingly powerful. The scariest part about them is that, even in a Crapsack World like the Berserk universe, they will make things much worse if they come to power.
The Neuroi from Strike Witches. They came en masse, massacred humanity without a word of communication, covered the land with miasma that ate at the crust of Earth until it shattered, and pushed humanity to the point where sending teenage girls into combat with them was the only viable option remaining.
Marder from Panzer World Galient, in a sense. The Panzer technology acquired by his army allowed him to take over the Volder kingdom, since Arst's culture and technology is far more primitive. Only when Jordy stumbled across the Iron Giant Galient could the world's populace stand a prayer against his forces. As it happens, Marder actually hails from the artificial planet Lanplate (which is inhabited by the descendants of former Arstians).
In Majin Tantei Nougami Neuro, you'd expect the next major villain to be a demon, since Neuro is a demon and all. Only one other demon is ever shown in the series and Neuro easily controls him. Instead, the series goes in a completely unexpected direction by making the first truly major arc follow a super powerful AI that can turn people into criminals and slaves via brainwashing. How do they top that? Six humans who are really, really evil. That evil is where they get their superpowers, in fact. A series about a demon detective never once goes the supernatural route.
Celestial Being from Mobile Suit Gundam 00, as seen from the perspective of the Superpowers. No one expected a force of high tech mobile suits to show up and tip the status quo. Even more unexpected is that Celestial Being's founder shows up to give a speech, after being supposedly dead for centuries.
The One Year War in the Universal Century Gundam shows in a sense started out as this. The Federation didn't expect just how powerful and game-changing the use of mobile suits were, which explains why Zeon was able to get away with stuff like Operation British and even an invasion of Earth. But once the titular Gundam itself goes operational and the Feddies developed their own armies of mobile suits, the tables turn.
The D-Reaper of Digimon Tamers. The series' writer decided that the final boss would be neither Digimon nor human. The result was something that the heroes or the audience would have never expected.
Each new Dragon Ball villain tends to be this to a varying extent, but special mention goes to famous Evil Overlord Frieza whose power advantage over all the protagonists (and antagonists) combined was akin to helpless mortals opposing a god. Even though later villains could make mincemeat out of him, they almost always started out in a similar "tier" of power to the heroes; Frieza started out several tiers ahead.
In Pokémon: Diamond and Pearl Ash and his friends once encountered an actual ghost. While there are many Ghost type Pokemon, the one they faced was a human ghost that was going drag them into its realm.
Toriko has been a simple Good vs. Evil story of the benevolent IGO vs the monstrous Gourmet Corp, which is why, a third power, consisting of hidden agents within both groups, collaborating with wealthy folk called NEO take everyone off guard.
The Titans of Attack on Titan are Humanoid Abominations that legend states literally appeared out of nowhere one day, and began to devour humanity to the brink of extinction. In the centuries since, humanity has learned only a few precious bits of information about them and that merely increases the mystery around them. The massive, 50m walls that surround humanity's last stronghold protected them for a century — and then one day, a 60m Titan appeared out of thin air and kicked a hole in the wall, allowing the normal-sized Titans to enter. Attempting to learn their origins and why certain humans like Eren can transform into Titans is one of the driving goals of the series.
Even among the Titans, the Beast Titan is inexplicable. It's a 17m giant that looks more like an ape than a human, is far more intelligent than its kin (to the point it can speak fluently), and seems to possess the power to transform humans into Titans. There are hints that the Beast Titan is responsible for everything humanity has suffered, and given its abilities, it may be the only true Titan in the world.
Not quite a villain, but Kuya and the nation of Kunnekamun in Utawarerumono mark their entrance into the plot by walking all over the various medieval Japanese nations with their state-of-the-art Humongous Mecha.
The storylines in Ramba normally dealt with mobsters, drug dealers, mercenaries, etc. In "Vendetta From Hell", Ramba fights a black magic coven that summons a demon in an attempt to kill her. This was the only appearance of the supernatural in the series.
Fighting (and beating) cosmic beings may now be passé in superhero comics, but in its original context the "Galactus Trilogy" from Fantastic Four fits this. The appearance of an all-powerful "villain" that was beyond good and evil, and who immediately put the protagonists in a literally helpless situation, was unprecedented in superhero stories at the time.
The Human Torch: We're like ants... just ants... ants!!
After Age Of Ultron, Galactus has taken this to another level — he's been displaced to the Ultimate Marvel universe. Cataclysm The Ultimates Last Stand begins with him appearing out of nowhere and vaporising a chunk of New York without so much as an "I HUNGER." The Ultimates only start to understand what they're dealing with after Tony Stark matches his energy signature to 616 Peter Parker.
In Watchmen, a giant squid monster attacks New York, and the world governments unite to fight this terrible threat. The all-too-human Big Bad created the alien-looking monster as a Batman Gambit to prevent human extinction through nuclear war.
Dr. Manhattan serves as a non-villainous equivalent. He's the only Super in the world, and sports godlike powers. World politics are changed forever when he shows up. This leads to moments like him ending the Vietnam War in about a week, and the escalation of the Cold War because the Russians are scared shitless. A noted scientist makes the comment that absolute terror is, in fact, the sane response to the existence of such a being.
In the "burnt offering" arc of Cable & Deadpool, Cable is kicking the collective asses of Deadpool and the X-Men. The authorities call in... the Silver Surfer, whom even Cable didn't expect, resulting in an epic beatdown and eventual semi-depowering (even though Cable breaks the Surfer's board). This is notable since the Fantastic Four and X-Men characters rarely interact, so the Silver Surfer (who rarely intervenes in Earth's affairs even within Fantastic Four storylines) appearing really was a surprise.
The Anti-Monitor in Crisis on Infinite Earths was out of context for the entire DC Multiverse. A being that could and did successfully annihilate nearly all the universes and forced the heroes to collapse the five remaining universes into one, forever transforming the DC Universe and everyone in it. His power was so overwhelming even an assemblage of the mightiest beings from all remaining worlds proved little more than a distraction. Even with its shell torn away, its power drained, and its power source dismantled, it took Superman and Superboy (along with some help from Darkseid) to finally finish it off... which in turn triggered a supernova. He was that nasty.
In Captain Atom: Armageddon, Captain Atom is essentially an out of context hero to both the Authority and the entire Wildstorm universe.
Bane functions this way in Batman: Knightfall. A villian who has been cut off from the outside world for almost his entire life, his existence is at best an urban legend to most Gotham City natives. When he murders six prostitutes and carves images of bats into their flesh, the Gotham police naturally blame Batman. Even after he and his gang launch rockets at Arkham Asylum, enabling the world's most dangerous criminals to escape and wreak havoc on the city, most Gothamites are too preoccupied with trying to stop The Joker, Two-Face, Poison Ivy, and all the rest that they remain ignorant of Bane's ultimate plan for the city: to permanently cripple Batman, seize control from Gotham's mob bosses, and rule over the city as its "king."
Doomsday showed up out of freaking nowhere to curbstomp most of Earth's heroes before going off to accomplish what no one else dreamed was even possible: kill Superman.
Chaos appears randomly in the middle of Metropolis City, uses his ability to induce extreme fear in his opponents to catch the Freedom Fighters off guard completely and kills Johnny Lightfoot, becoming the only villain to successfully kill a Freedom Fighter.
Colonel Granite and Operation Starwatch also serve as this, being completely unknown to Mobius par the Freedom Fighters leading an Alien Invasion from Planet Earth, invading Mobius, trouncing the Freedom Fighters with superior firepower, and planning to sell off the conquered Zones to human industrial developers (and rename Mobius "Planet Percy" after his first name).
In W.I.T.C.H. the girls faced Prof. Takeda, a Mad Scientist who plans to wipe out all magic because his daughter was put in a coma because of it.
Inverted in Paperinik New Adventures. Paperinik and his enemies usually have human-like abilities and similar technology level to what Paperinik has access too, but Xadhoom (who, thankfully, is on Paperinik's side) is literally a Physical Goddess, with enough firepower to destroy city-sized warships in one shot and devastating planets in minutes while holding back and effective invulnerability to anything.
Fenris from Lucifer is known, vaguely, by many of the characters, but since the conflict and all of the big hitters are Judeo-Christian in origin very few of them take a minor character from a forgotten religion very seriously. Lucifer himself warns them not to underestimate the guy and still ends up getting outplayed and very nearly killed, and Fenris eventually ends up with the largest major character kill count and a very good claim at being the Big Bad.
One A Nightmare on Elm Street comic had Freddy deal with this, when the teenagers he's after try to destroy him by summoning an ancient Mayan monster that can dwell within dreams like he can.
Freddy: What the fuck?
Transformers: More than Meets the Eye: The Ammonites are introduced, they're a race of smaller living robots in an even longer war than the Cybertronians. It's revealed that they are the Decepticon counterpart of their race, and they've infiltrated and have been stealing technological improvements from the Autobots for some time. Come Transformers Dark Cybertron they've gone on the offensive against the bots.
This occurs freqently in crossover works. Characters from series A have experience in dealing with the threats and factions associated with their series. They also have a view of how the world works and what is or is not possible based on their experiences and which may be an accurate view of the world in the source material for series A. Then the author introduces characters and elements from series B which has different rules or power levels. In some cases, this works both ways as not only do the A-characters not know what to make of the B-characters, but the B-characters are also surprised by aspects or abilites of the A-charactes and the world they move in.
Inverted in Finishing The Fight, where the capabilities of the Master Chief and UNSC technology are beyond the ability of most of Faerun to combat.
Played with in Dungeon Keeper Ami. Sailor Mercury is transported into the World of Dungeon Keeper and has a rather unconventional approach to being a Keeper, as well as the whole evil alignment. She's more like an Outside Context Stealth Hero.
Tamers Forever Series: The Triad never considered Daemon returning as part of their plan. Naturally, this proves to be a catastrophic error.
Secret War: you thought Taryst was the Big Bad? ehh! wrong! It's Inquisitor Edracian who's behind everything but it's a subversion as many characters excluding Attelus and a few others knew of him and his involvement already.
In the The Culture/Harry Potter crossover Culture Shock, the Culture finds it hard to believe that Potterverse wizards, for all they appear primitive, can manipulate both layers of the Grid simultaneously, something only an even more advanced faction had previously demonstrated, nevermind things like the moving paintings that they can't even explain.
The Harry Potter fanfic "The Squad", the British Army is this to the wizarding world. The titular squad is a group of SAS Commandoes sporting state-of-the-art anti-terror training and equipment. Let's just say high-powered scoped sniper rifles, assault helicopters, and claymore mines are all great equalizer when it comes to Death Eaters and their wands.
Queen Chrysalis in the Wedding Arc is this intentionally, having spent years enforcing The Masquerade while systematically infiltrating Equestria on every level so that her invasion would go off without a hitch. However, she then ironically becomes a victim of the inverse of this trope, as numerous ponies she didn't bother to view as a threat have Misfit Mobilization Moments and begin to throw wrenches in her plans.
The Master of Death: Outsiders are this by definition, but even discounting what Potter specifically can do, Potterverse spells can do things like transfiguration that the Dresdenverse has no conception of.
Death Note Equestria: Thanks to the powers of the Death Note (which even she doesn't fully understand), Twilight Sparkle as Kira becomes this to the entire Equestrian government. That said, just as L is figuring out the limits and rules of her powers, the golems suddenly show up, taking both sides by surprise.
In Magical Pony Lyrical Twilight the Equestrians are this to the TSAB and their High Council, being naturally-occurring (as opposed to deliberately-engineered) nonhuman sapients who are not servile familiars and having abilities the Bureau has no experience with. The fact that their entire species can use magic in one way or another probably doesn't help.
Star Wars: Paranormalities: Let's just say this story has that title due to thriving on these. The Valkoran Empire seem pretty normal for the most part at first, initially believed to be pirates/political terrorists before being revealed to be cultists, but their leaders are something else entirely. Maesterus is a Force user who isn't actually a Sith Lord (despite dressing similarly to one) with Lovecraftian Superpowers, Juganak is strong enough to dismantle a walker with his bare hands, Neur is a brain-damaged human-Twi'lek hybrid, Machinus is a droid with the soul of a Nautolan, and Masochus is an insane ex-Sith Lord who skinned himself down to the bone. Let's not even get started on Valkor himself...
The Forceless Collective, an army of Eldritch Abominations from another galaxy that can possess other living creatures and it's theorized that there are other Forceless born from the Force wounds created by mass genocides. Like the Yuuzhan Vong, very few in the galaxy knew about their existence aside from the Valkoran Empire.
The ashes were trampled into the earth, and the blood became as snow. Who knows what they came for... weapons of steel...? or murder? It was never known, for their leader rode to the south... No one would know that my lord's people had lived at all.
Common in Batman films:
The Joker is this in The Dark Knight. In the conflict between Batman, the cops, and organized crime, all with their own brand of rational goals, nobody was prepared to deal with a mastermind who was exclusively in it For the Evulz.
At the beginning of the 1989 movie Batman, the city officials are concerned with Boss Carl Grissom and want to nab Jack Napier only because he's Grissom's "number-one guy." Even after Napier has become The Joker and killed Grissom, and he and his goons have targeted them for assassination, Vinnie Ricorso and his lackeys think that Grissom is still alive and are busying themselves with taking care of his operations while (they think) he's on vacation. It takes until almost the end of the movie for the media and the police to finally confirm that Grissom is dead and that the Joker has taken control of Gotham City's underworld:
Joker:Joker here. Now, you fellas have said some pretty mean things, some of which were true, about that thief, Carl Grissom. He's dead now, and he's left me in charge."
Much like in the comics, Bane's arrival in The Dark Knight Rises is unbelievably downplayed by the police, considering him just an overblown gangster; when chasing his crew after a terroristic assault on the Gotham Stock Exchange, the police force immediately start ignoring him when Batman reappears and diverts nearly every cop in the city to the chase, letting everyone Bats hasn't taken out himself escape. Even when Jim Gordon was brought to their hideout the concept of a literally underground army is laughed at and dismissed out of hand.
This is how the aliens are viewed in Cowboys and Aliens. As a result, they're initially referred to as "demons", something the cowboys do have context for.
Dick Tracy: The Chicago police believe to the very end that Big Boy Caprice has kidnapped Tess Trueheart, even after it has become clear (to the audience) that The Blank has become the infinitely more dangerous threat to the city. (And since Breathless Mahoney is killed in the climax, she proves to be The Greatest Story Never Told.)
Battleship involves an international naval exercise being interrupted... by alien ships coming from underwater to seal an island chain in an impenetrable force field, leaving three destroyers to fight them.
Loki in The Avengers is, as SHIELD agent Natasha Romanova (aka Black Widow) puts it, "nothing we were trained for"- most of the eponymous superteam are used to terrorists with fancy weapons, not mad physical gods from Another Dimension. Fortunately, Loki's elder brother Thor has dealt with his crap before and joins the human heroes.
One could argue the Chitauri experienced this as well, since it's clear they were expecting to simply waltz in and easily conquer the human race. Instead, their invasion is repelled in only a few hours by a team comprised of two Badass Normal soldiers, an Asgardian warrior, a guy in powered armour, a super-soldier... and the Hulk. Best summed up in The Stinger;
It could be argued, by way of Alternate Character Interpretation, that Jennifer (Reese Witherspoon) is this to the townspeople in Pleasantville. She and her brother, after all, have literally arrived from Beyond The Fourth Wall, and simply by existing (okay, and also by actively engaging in her usual promiscuous behavior after her brother explicitly warned her not to) she corrupts the very fabric of Pleasantville, changing everything. It is interesting that the film portrays the townspeople as the antagonists when, in their own minds, Jennifer is the one responsible for goading them to violence (and the very fact that they have become violent is her fault too, since she has literally Taught Them Anger). Even the townsfolk's discrimination against "colored" people, which is supposed to be understood as Fantastic Racism, can be interpreted as a vulnerable population simply trying to protect themselves against infection by a sociopathic "typhoid Mary" with an apparently sexually transmitted disease that is causing people to (by their standards) horribly mutate. Thus, the courtroom scene is not segregation; it's simply quarantining.
How the aliens in the prologue of The Fifth Element are seen by the archaeologists, however incorrectly.
Imhotep in The Mummy 1999. He was an Ancient Egyptian priest who was mummified alive and cursed. The result of this curse is that, when he comes back, he's practically invincible and no one except for the Medjay really know how to deal with him, and even the Medjay have no way to stop him on hand—their whole presence near Hamunaptra was to keep him from getting out in the first place.
This is the entire point of the movie Predator: five heavily-armed military men hunting down a missing cabinet member when suddenly... technologically-advanced alien hunter!
Nobody in the Pacific Rim universe was prepared for The Kaiju, giant city-destroying monsters. Likewise, The Kaiju and the aliens controlling them were not expecting humanity to come up with giant robots to fight them with or for one of those robots to be able to breach the rift with a nuke and blow them up.
This is a major plot point in Foundation and Empire, when a man called the Mule shows up out of nowhere and starts conquering planets. Hari Seldon's predictions, which have been infallibly running the show for centuries, are suddenly no longer accurate because he could not possibly have foreseen the Mule's arrival, as the Mule is a mutant. However, Hari knew that something was bound to happen in his thousand-year plan, so he put together a secret team to make sure the unexpected could be fixed. The fact that the plan still works on time after the Mule is defeated is a tip-off to one protagonist that something is up.
By the end of Foundation and Earth, Golan Trevize comes to the conclusion that this trope is the main reason why he choose Gaia over the Second Foundation — Psycho-History and the Second Foundation's means of manipulation and planning are based on human behaviour (the Mule thought like a human, he just had an ability others did not), leaving them open for problems if faced with truly alien ways of thinking.
When you say, "Space adventure about a magical force," you (impassively or fondly) think of Star Wars. When you say, "religiously sadomasochistic alien zealots," you blank out. When you add "that are immune to The Force", you get the Yuuzhan Vong. Extremely unusual addition or not, those guys dominated a large portion of the post-Palpatine era. A subversion might come into play, since there are theories that Palpatine, having foreseen the invasion through the Force, orchestrated the Clone War and the Galactic Civil War specifically to prepare the Galaxy.
The same goes for Thrawn. A Chiss (blue-skinned humanoid)? As an Imperial Admiral in the xenophobic Galactic Empire? With chess-maneuvering that's soDangerously Genre Savvy that he gives Darth Revan a run for his money? Who happens to be the most respectable, even likable villain thus far in Star Wars history?
The Seven Kingdoms are ripping themselves apart in civil war, blissfully unaware that the demonic Others are amassing their army of the undead just north of the Wall. Only the Night's Watch has taken any steps to fight them, and they are woefully outnumbered and much of the knowledge they used to have about the Others has been lost.
Mellissandre and her red god R'hllor. She's dismissed as a witch and a heathen, but she's got real power that quickly shifts the tides of the War of the Five Kings.
Aegon the Conqueror, who arrived in Westeros from distant Valyria and quickly conquered six of the seven kingdoms in a series of Curb Stomp Battles due to his use of dragons. Particularly Harrenhal, a massive impregnable fortress that was built to withstand any invasion by land, but was absolutely defenseless again dragons.
Although the people of Westeros hear rumors about Daenerys Targaryen, the Mother of Dragons and pretender to the Iron Throne, no one expects the return of Aegon Targaryen, son of Rhaegar, who was presumed slain during Robert's Rebellion. He suddenly lands in Westeros with an army of elite mercenaries without any warning. Even the reader doesn't know about him until midway through the fifth book.
In the Shadowleague books, Lord Blade is this for the people of Callisoria, and possibly even his fellow Loremasters.
The Vord in Codex Alera come as a nasty shock to the Alerans, who thought all they had to deal with was the Marat, the Canim, the Icemen, and each other. The only information about them the Alerans have is bits of nearly-forgotten Marat folklore from the last time they almost ate the planet.
The premise of the Worldwar series has World War II being thrown into confusion when the alien Race arrives with its invasion fleet, forcing former mortal enemies to fight together to save humanity. Oddly enough, this works both ways - the Race had been expecting the same knights on horseback their probes found a mere seven hundred years earlier. But not only have the natives gone on to invent tanks and airplanes, they've also devised weapons the Race never conceived of, like chemical warfare, suicide attacks, and wet-navy warships. Combined with mankind's extreme tenacity, fanaticism, and potential for cruelty, the Race consider just glassing the damn planet at least once a book.
The Seanchan in The Wheel of Time, are an empire of conquerors from beyond the sea, founded by the son of a great king from a thousand years ago who sent an army sailing to the west. They appear for the first time in the second book of the series, but even four books later most people in the known world don't believe in them.
In the final book Shara is an even bigger example of this, surprising EVERYONE (except the readers).
The characters of World War Z repeatedly lampshade that nobody even believed in zombies, let alone knew anything about how to defeat them. note Hilariously not the case in Real Life: The Military does plan for things like zombie outbreaks specifically as thought exercises so they'll be ready for Outside Context Emergencies.
One interview segment includes a non-zombie example: early on, Iran managed to remain relatively secure thanks to advantages of natural terrain, but their attempts to stop the flow of refugees from neighboring Pakistan by blowing bridges at the border enraged Pakistan's government. The interviewee describing the situation talks about how longtime enemies India and Pakistan have well-oiled diplomatic channels established to prevent their two countries from escalating into full-scale warfare, but the lack of any historical enmity between Pakistan and Iran meant that there were no such measures in place between them - resulting in a nuclear war that destroyed both countries.
In Triplanetary, the first book of the Lensman series, the heroes have escaped from the clutches of the villainous Gray Roger, figured out his nefarious plans, have mustered the space cavalry, and at last have his evil forces on the ropes — and then out of nowhere a brand new super-advenced alien species called the Nevians barges in on the battle, easily trounces every ship with its ability to partially neutralize inertia, and kidnaps the heroes several light-years away. This signals the beginning of the Lensman Arms Race.
H. G. WellsThe War of the Worlds. This trope works in both directions. The humans had no idea about the alien invaders and the alien invaders had no idea about human diseases.
In The Excalibur Alternative, the heroes are a medieval troop who none of the alien races they are meant to subjugate can really touch. To the heroes themselves, the aliens that abducted them were this.
The Mesan Alignment from Honor Harrington. For all the experience the heroes have fighting their proxies, those are just that: catspaws, pawns, disposables who know not of their true masters. They have plans on plans on backup plans stretching centuries, claws sunk into places no one expects and their technology breaks the rules the rest of the galaxy has comfortably become used to.
Subverted in Harry Harrison's Invasion: Earth, when an alien craft rumbles through New York and crash-lands in Central Park. The military shows up prepared to enter the craft. When asked, the guy in charge simply states that they're following established protocol for exactly this sort of situation. It's likely this is also true in Real Life.
In Hell's Gate, both the Union of Arcana and Sharona are this to one another. The Arcanans are a society based on magic, with their most advanced mechanical weapon being the crossbow, and they run into the Sharonans, who pack World War One-era firearms and artillery that utterly devastates the Arcanans, as well as Psychic Powers that give them an edge in communication and seeking out threats and deceptions. On the other hand, the Sharonans are entirely unprepared for enemies who wield magic, including concealable crystals that can spit lightning, magical computers and surveillance devices, and dragons.
The New Republic in The Eschaton Series is essentially 19th century Prussia IN SPACE, trying to pretend The Singularity never happened. It is therefore unequipped to even understand the Festival, which is the Edinburgh Arts Festival hopped up on nanotech, much less defend against it.
From the point of view of the bad guys (and readers), this is what happens in Weber's Out of the Dark. So you got your typical science-fiction alien invasion of Earth opposed by assorted teams of Ragtag Bunch of Misfits, but there's really no way humans can win, since genocide by biological warfare would be fairly easy for the aliens if things get too out of hand...and then freaking Dracula decides he's getting tired of all this alien shit.
In the Mistborn series, up until the end of the second book, everyone has been dealing with understandable threats: The Lord Ruler was a badass but defeatable foe in the first book, while the various kings struggling for power, including the army of koloss, were predictable and understandable, if dangerous and well-armed, foes. Then in comes Ruin, who is a literal god of destruction and unmaking.
The appropriately named Outsiders from The Dresden Files, who come from outside reality and do not play by the normal rules that govern supernatural beings. Particularly Nemesis, an entity that can infect people's minds and warp their personalities to sway them to the Outsiders' cause. It can alter the fundamental mental nature of the beings it infects, such as removing the Cannot Tell a Lie restrictions that normally bind the fae, something that everyone believes to be impossible.
Karl Schroeder's science fiction works, especially Lady of Mazes. A recurring theme involves small societies whose ancestors exiled themselves from an all-encompassing transhuman future full of godlike artificial intelligences that manage everything. These societies strongly restrict technology and knowledge to keep from accidentally growing the AIs all over again and try to provide meaning for their people's lives, to the point that after a few generations the people have completely forgotten any other way of life existed. And then the outside world comes for them, unable to tolerate a pocket of humanity that does not take part in their "enlightened, perfect" transhuman society.
In Sourcery, Coin the Sourcerer walks into Unseen University and starts altering the whole world with limitless magical power, the first sourcerer to show up in centuries. Discworld's wizards normally have to work within fairly consistent rules and limits, largely because they can only draw upon and channel natural background magic that already exists in the environment; sourcerers can generate magic -or at least draw it in from Somewhere Else where it's functionally infinite- completely at will, meaning that they can brute-force reality itself by sheer power until the only explanation for what they do is A Sourcerer Did It. This is highlighted by the fact that even Lord Vetinari is caught completely off guard and spends most of the book as a small lizard. His credentials as a schemer and anticipator have not yet been established at this point in the series, but even if they had, there's no reason he would ever have anticipated this.
In "The Depths of Shadows" by Jack Butler, a hardened team of heavily armed, heavily cybered up street samurai walk right out of a Willian Gibsonesque world into a Dwindling Party nightmare when they encounter an honest to God vampire.
Grantville was this to the European nobles in 1632. After all, you normally don't plan on a town from the future full of advanced weapons and odd notions of how the world should work to be transported into 17th-century Germany.
The Borg from Star Trek: The Next Generation. In their first appearance, Q uses them to give the crew of the Enterprise a lesson in just how dangerous the universe still is and how "prepared" they are.
Interestingly, Species 8472 is an Outside-Context Villain for the Borg: a species from another dimension that they can neither assimilate nor destroy. It proceeds to kick their asses.
Angel had many examples of this trope. The first was Sahjan, whose presence was not even explained to the audience until his final episode. Then there was The Beast, the cast given only vague warnings about its arrival and were outclassed by it in every possible way. Then there was Jasmine, who had even less warning and was so beyond their experience the only way they acquired information of her at all was due to a visitor from her home dimension.
And then things really get bad when Illyria wakes up. Her two episode introduction is more or less devoted to a long realization that this really is a horrible LovecraftianPhysical God, not a poser, and that things like pointing guns or swinging swords at her are really quite quaint.
And then things got sort of better when her intro ends with Illyria realizing that the passage of time has already defeated her. She ends up staying with the heroes because she has nothing better to do, with her army and her worshipers long since dead.
Inverted by Warren Mears. Used to dealing with vampires, demons, and gods, Buffy wasn't prepared to deal with one Ax-Crazy human Mad Scientist.
Even before Warren Mears, there was Ted, the titular killer robot from the episode "Ted". Buffy knew how to handle vampires and demons and things that went bump in the night, but a killer robot who pretended to just be a guy? She had no idea how to deal until she figured out his secret.
Inverted in Doctor Who. The Doctor is an Outside Context Hero. To the extent that a large group of his enemies, none known for working well with others, pool their resources and abilities to trap him in the ultimate prison, The Pandorica.
The Doctor himself has encountered something like this in the "midnight entity," a creature so obscure and dangerous that it completely owns the doctor and he knows absolutely nothing about it. It's so bad that the Tenth Doctor was never quite the same after meeting it.
The Silence perhaps. The Doctor routinely sends aliens packing in what comes across as not a long time, hours or days at most. He, Rory, Amy, and River Song spent three months working to defeat the Silence, and even then they turned up in later episodes. The fact that people, The Doctor included, forget the Silence entirely as soon as they stop looking at them makes them not exactly easy to fight.
In the 2012 Christmas special Clara is an Outside Context Companion. She constantly surprises The Doctor who finds her extremely unique and fascinating. When he first shows her the Tardis, she throws him for a loop when she refers to it as being "smaller on the outside" which while true is a inversion of the usual human reaction to the concept.
The Doctor is this trope completely straight from the point of view of the villains.
Alphas villain Marcus Ayers explicitly calls himself - and all other Alphas - an "out-of-context problem" for normal humans. He then fatalistically points out that only way humans know how to deal with such a problem is to destroy it, which they try to do to him shortly afterwards.
When you think about it, the humans/Earthlings/Tau'ri of Stargate were outside-context problems for the Goa'uld: what god-pretender could even conceive of a ragtag bunch of explorers from a backwater planet (Projectile weapons? Chemical rockets? Really!) first wiping out the overlord on their first trip offworld, then setting out to systematically wipe out the rest of them?
Andromeda had the Magog, who were originally Outside Context Villains, since they came from beyond known space. The Spirit of the Abyss turns out to be a whole new layer of Outside Context Villain on top of the Magog. The episode "D Minus Zero" reveals that the Highguard have a protocol to deal with Outside Context hostiles: Step One is to gather information. You need to find out who they are, what they want, and what their capabilities are. Only then can you figure out what to do.
Several episodes of Supernatural deal with crazy humans, leaving Dean bewildered. He even lampshades that he can understand all sorts of supernatural things like ghosts, vampires, demons, etc. It's humans he has trouble dealing with.
Blake's 7 very nearly had this happen in Series 2, where at one point the intention was for the arriving alien force in that series' cliffhanger to be the Daleks.
This is subverted and then inverted in Justified. Quarles is made to appear like a mysterious and dangerous Outside Context Villain but after the main characters figure out who he is, they are able to thwart him since to them he is just another "carpetbagger" like countless others who have come to Kentucky in the past. In turn Quarles starts to realize that he is completely unprepared to deal with a lawman like Raylan or a devious criminal like Boyd.
Short-lived seriesThreshold was premised on the US government turning to the plans of the one person for whom alien invasion was not an Outside Context Problem. Many of the complications with her plans come from either the aliens being more insidious than she'd anticipated, or resistance and disbelief from everyone else for whom the aliens are completely outside their context.
from a Earther perspective, the Minbari: Earth Alliance knew of their existance and their fame and could conceive their firepower (on a similar level of that of the Centauri warships, that Earth Alliance knew of), but had no idea that Stealth in Space was even possible. The end result was an Hopeless War in which Humans were considered incredibly Badass for forcing the Minbari to actually try to annihilate them instead of just waltzing in and winning automatically, and would have ended with the complete extinction of Mankind had the Minbari not changed their mind at the last moment;
the Shadows. The first time we see them, one of their warships appears from literally nowhere and disintegrate a Raider ship for no apparent reason, and one of their emissaries gives the Raider's loot to Londo. It takes a while for the good guys to realize even their very existance, or how powerful they actually are;
the Thirdspace Aliens, who, in the distant past, nearly subjugated every single sentient in the galaxy, appear from nowhere with ships that could take on both the Vorlon and the Shadows and telepathic powers so immense that they could brainwash even the Vorlons (until then the most powerful telepaths in the series), and their scouting party is barely defeated before the gate enabling them to show up is destroyed.
Initially, the Goa'uld themselves. The Earthers thought the one they'd killed in the movie was a Last of His Kind and that they'd eliminated any threat to Earth when they took it out. Not so much...
The Replicators, an extragalactic, mechanical Horde of Alien Locusts who make all kinds of trouble for SG-1 and its allies and eventually invade the Milky Way. By then SG-1 had some experience with them, but the Goa'uld still saw them as this trope.
Anubis, whom the System Lords thought had died eons ago after his banishment. Turns out he was Not Quite Dead. His return in Season 5 forces both the System Lords and the Earth/Tok'ra/Free Jaffa alliance to shift their priorities from each other to the new enemy.
The Ori in the last two seasons.
In Lost Girl, the Garuda catches everybody by surprise because it predates the Fae. There was no myths or legends of it, so there is nothing to reference. However, a few people like Lachlan knew about it and had been preparing.
The last half of season 2 of Once Upon a Time is shown to be controlled, at least in part, by Peter Pan. While people on both sides of the fourth wall had probably been expecting him since Captain Hook showed up, it's doubtful they though it'd be as a villain. The first hint we see of him is his disembodied shadow coming to take lost and forgotten boys to Neverland, and even when he is finally shown in person, he's still different from anything they've experienced before. He controls Neverland completely, he can out-gambit Rumpelstiltskin, manipulate people without trying, and even those who have faced him before are unsure how to defeat him, or even if he can be.
Agents of S.H.I.E.L.D. shows that S.H.I.E.L.D. has a name for Outside Context Problems: 0-8-4, code for an object of unknown origin and utility. Thor's hammer was one, and a laser weapon found in some ancient ruins was another. Obviously, eventually sometimes context is provided; they still don't know much about Mjolnir, but they know where it came from and who it belongs to. Likewise, the laser weapon turned out to be a device commissioned from HYDRA during WWII.
The music video of Skrillex's First of the Year has a child kidnapper very surprised when said child summons a demon to kill him.
Exalted has quite a few of these. In the past five years, Abyssal and Infernal Exalted — types of Exalted no one's seen in all of history — have started crawling out of the woodwork after their respectivebosses got their hands on half of all the Solar Exaltations ever crafted. And for the recently-returned Solars, the eventual return of the Scarlet Empress can seem like this... especially since she's now a puppet for the Yozis.
The Abyssals and Infernals apply doubly so to the Sidereals, who were watching the shop while the Solars were dead and the Lunars were on the run. They have the ability to track all things which reside within Fate... which the Abyssals (who have technically died and surrendered their fates) and the Infernals (who were reforged in Malfeas) don't count under.
The quintessential example might be the conquest of Thorns. An army of ghosts and undead, led by the horrifically powerful ghost Mask of Winters, supplemented by the aforementioned Abyssals (being seen for the first time) and a gigantic dying monster, leading to the city being not only taken over, but converted into a Shadowland expanding at a terrifyingly unprecedented rate.
The event of the Alchemical Exalted (or Autochthonians in general) entering Creation would play out like this in scenarios with a military context. The reverse holds true as well; the Autochthonians have very little idea what Creation is actually like and it disturbs them fairly badly.
The history of the Iron Kingdoms is this: people puttering around with warriors, wizards and the like getting steamrolled by The Empire with seriously high sorcery Power Levels from across the western ocean. It took the creation of "scientific" items such as Gunpowder, Steam engines and War Machines four hundred years later before The Empire finally got driven off
The Eldrazi in Magic: The Gathering, being Eldritch Abominations from the spaces between planes of existence which feed on said planes, and don't obeythe basic rules of magic. Until their escape, the plane of Zendikar where they were imprisoned was presented as an adventure world. To quote the Rise of the Eldrazi Player's Guide, "Previous quests have been for treasure and glory. In the new Rise of the Eldrazi set ... only one goal remains: survival."
Also the case for New Phyrexia's attack. Even when the Mirrans knew they were at war, they expected their opponents to wage war on the people... not the ecosystem.
Standard Imperial policy is only so outrageously cruel and draconian because otherwise they would get suckerpunched by every out of context problem in the galaxy (for reference, soul-eating psychic jellyfish out of nowhere are one of the more expected, planned-for, and familiar threats). And they're still getting suckerpunched.
Slaanesh for most of the Eldar. Some seers tried to warn their people that their hedonism was feeding a gestating god, but few listened. Those who did hid inside the Webway or built Craftworlds to flee in, but they did not understand just what would happen when Slaanesh was "born." The god's birth tore a hole in reality, plunging the heart of the Eldar empire into the Warp and instantly consuming the souls of almost the entire species. Most of those who fled did not make it far enough to escape having their souls eaten. And while those hiding in the Webway initially seemed unaffected, they soon discovered that Slaanesh was still consuming their souls, just very slowly.
Baba Yaga was this to the Linnorm Kings in Pathfinder. She suddenly arrived from Earth in her Dancing Hut one winter 1400 years ago, conquered half their territory with her army of trolls and fey, established one of her daughters on the throne, and just as quickly left, leaving her army behind to protect the newly-established kingdom of Irrisen. Reign of Winter even reveals why she bothered; she sustains her immortality by consuming the Life Force of her female descendants/daughters. Irrisen, then, ensures she always has a steady supply of that precious bloodline protected and kept ready for her when she needs a pick-me-up.
In "Star Control", the Ur-Quan (either flavor) would roam the galaxy killing and enslaving vastly inferior races. A long time ago, there were the Dnyarri with their lightning takeover of the Milieu. The Androsynth totally got Outside-Contexted by the Orz. And the Sa-Matra was far beyond any resistance until Chenjesu took the drastic step of combining their species with the Mrnmrhrm so as to form a super-race capable of facing it.
Star Ocean: Till the End of Time has the Executioners, who roll into the galaxy and start destroying everything, apparently sent by masters from beyond our reality to destroy us all, and an order of magnitude more powerful than anything else faced up to that point in the game, with ordinary enemies rivaling bosses in difficulty - if they can be beaten at all. It is even more out of context than it appears at first glance. The characters go to a Cool Gate to travel between worlds, using the overpowered magical abilities that their parents gave them to break their way out of our world and into the world of the Executioners' masters... whereupon they end up dumped in what seems to be an amusement park and fight some guards who you handily beat, them being little better than mooks compared to the characters. They discover that the world that the game has been taking place in is a video game made by people in 4D space, and the Executioners are nothing more than programs sent to clean up the errors which have been accumulating in the game world by deleting everything.
Final Fantasy games are fond of this, with the villain often being something utterly alien to the protagonists:
The Cloud of Darkness from Final Fantasy III is familiar to the World of Darkness, but wholly unknown to the World of Light.
The Lunarians (specifically, Zemus, Golbez, and the Lunarian Lost Technology) in Final Fantasy IV, which include the hero, on his father's side anyway. He was raised as a human, so he's just as baffled by the powers of his father's people and the artifacts they left behind. There's supposedly mostly good Lunarians, but we only see one and a Face-Heel Turn.
Exdeath of Final Fantasy V is known to the inhabitants of the world he comes from, but utterly unknown in the other. Fortunately, people from his world follow to help the defenseless natives of the protagonists' world fight him.
The Terrans of Final Fantasy IX, which, like IV, include the hero, who, like IV, has gone native. Unlike IV, all the other aliens are of the "invade and help their planet devour the souls of those that live on ours" variety.
In Pokémon Mystery Dungeon: Gates to Infinity, the Bittercold is this for the entirity of the Pokemon franchise, being the first boss besides Dark Rust in Pokémon Rumble Blast that isn't a Pokemon or a Pokemon trainer. Instead, it is the personification of all of the Pokemon's negative emotions, given form because how much negativity has been going around in the Pokemon world as of late. It's a giant crystal... thing, who uses attacks never seen in the Pokemon franchise before, as well as causing Pokemon, and humans to have a hard time breathing when near it. On top of that, its only goal is to bring about The End of the World as We Know It in order for it to be recreated into a less bitter and vile one.
The Zerg from Starcraft, and the Burning Legion from Warcraft, who are a Horde of Alien Locusts from another part of the galaxy and an army of omnicidal demons from another dimension, respectively.
The Zerg are out-of-context for the Protoss more than anything, since they were running the galaxy as part of their "Great Stewardship". They never imagined a Horde of Alien Locusts coming out of nowhere with the explicit purpose of assimilating them, and destroying their ancestral homeworld.
The Protoss were pretty out-of-context for the Terrrans as well, the Terrans discovered they were not alone when a massive fleet showed up out of nowhere and sterilized one of their colonies.
The United Earth Directorate from Brood War may actually be a better example. The Zerg are at least comprehensible to the Protoss as they are also a creation of the Xel'Naga, and part of their power comes from absorbing the knowledge of the Xel'Naga. Terrans, as far as most of the Protoss are concerned, are a bit of background noise in their fight with the Zerg. But then a fleet from Earth shows up and (for a time at least) controls the Zerg and becomes the top power...
The Dark Voice and his Hybrids also seems to be this in StarCraft II, especially in the Bad Future: the Zerg were the main threat that everybody recognized, and then, just as Kerrigan was killed to defeat the Zerg, the Fallen One came in, took over the Zerg, and used them to bring everlasting darkness to the Universe.
In Spyro Orange and Crash Purple, the protagonists suddenly find themselves the victims of a villain switcheroo, and have to take on each other's archnemeses.
In the first FreeSpace, the two known races of the galaxy, the Humans and the Vasudans, are at war. Then suddenly, weird black ships (with Deflector Shields, something neither race thought possible) show up and start killing everyone. Turns out those ships belong to the Shivans, a race of seriously deadly Horde of Alien Locusts. Even after two games, the only things known about them for certain is that they're extremely technologically advanced and they always have way more power available than you think.
Similarly in Crysis, the Americans and North Koreans are busily having a scrap on an island and managing to ignore various weird happenings around the mountain in the middle of it, until suddenly the aliens leap out and freeze the whole place solid.
In Dragon Age: Origins the Darkspawn are this to everyone except the Grey Wardens and the Dwarves. Since it's been hundreds of years since the last Blight, the people of the surface believed that the Darkspawn had been eradicated. When the Fifth Blight strikes, the people of Ferelden are left scrambling to prepare their defenses and it doesn't help that Ferelden has so few Grey Wardens to help. Things get worse after the Battle of Ostagar — everyone is too preoccupied with serious internal problems including a civil war and underestimate the true threat level of the Blight. Nobody in Ferelden is really prepared to fight monsters that a) vastly outnumber them b) carry a lethal and corrupting magical plague and c) are controlled by an insane dragon god that is unkillable unless a Grey Warden strikes the final blow.
In Dragon Age II, Cassandra and the Seekers are desperately trying to figure out who out of all the key players in Kirkwall, was the Big Bad responsible for the outbreak of the Mage/Templar War. Varric tells her that none of them are responsible, but the Red Lyrium Idol recovered from the Primeval Thaig certainly was a key factor in what happened.
Few of the factions in Galactic Civilizations II even knew the Dread Lords ever existed, and no-one expected they would ever return.
Nobody in Valkyrie Profile 2 Silmeria expected that Lezard Valenth was actually a time-shifted version of himself from the future. By the time anyone figured it out, he had outwitted everybody, forcing the survivors into an Enemy Mine to beat him.
The demon from Clash At Demonhead showed up with little foreshadowing (unless you count the fact that he lives on Mount Demonhead), and mucked up things for both the hero and the bad guys. However, the hero kills the demon after a little sidequest, and then the plot picks up right where it left off.
The Reapers, like Sovereign from Mass Effect are this to the entire galaxy. They appear to wipe out all space-faring life every 50,000 years, and spend the intervening time asleep in dark space. Driven home in the Mass Effect 3 announcement trailer where it's made clear, given that the higher-ups constantly tried to silence his/her warnings about them, that no one besides Shepard knows what they are.
What makes the Reapers so devastating is that the scale and capabilities of the Reapers sits outside of the context of the Citadel's military doctrine. The three primary Citadel species have geared their militaries to cooperate and specialize, with each species supporting one another: the turians serve as the primary heavy combat element, supplying most of the ground troops, armored vehicles, and spacecraft. The asari provide elite biotic special forces and economic and diplomatic clout, at the expense of heavy combat units. The salarians provide advanced technology, intelligence, and covert operations units at the expense of heavy combat elements as well. This works just fine for the enemies that the Citadel is accustomed to fighting. But when the Reapers show up, they're so fast, they have such huge numbers, they have nonexistent logistics requirements, they have technology that at times breaks the laws of physics, and they have firepower and armor more powerful than anything the other races can even hope to achieve, which means they can attack anywhere at their leisure. As a result, the asari military gets smashed and the salarians only survive the majority of the war because the Reapers haven't bothered with them because their intelligence apparatus (geared to fight more conventional enemies) is a nonthreat.
In the Leviathan DLC for the third game, Shepard hunts for a mysterious Reaper-killer codenamed Leviathan. Instead of a rogue Reaper as the characters initially believed, the Leviathan are revealed to be giant aquatic lifeforms, with incredible mental abilities and a massiveGod-complex. They are also the race indirectly responsible for the creation of the Reapers, when a Rogue AInote (the Catalyst) turned against them and created the first Reapers in their image.
This trope also gets turned back on the Reapers in the form of Shepard. A member of a nobody species comes out of nowhere and absolutely trashes their plans...then, when killed off, comes back, tougher than they were before, and continues trashing. It's stated in the Leviathan DLC that Shepard is the first thing the Reapers have legitimately feared in millions of years.
The Wild Card Ending of Fallout: New Vegas makes the Courier themself this. While the New California Republic, Caesar's Legion, and Mr. House were busy scheming, some simple Courier who got shot in the head and left for dead crawls out of his or her grave, plays everyone for suckers, and forges a free and independent Mojave.
Caesar's Legion, on two accounts. All the other factions have been working for at least a hundred years, but the Legion showed up just 30 years ago to conquer Arizona and hasn't stopped. Caeser actively invoked this by basing his army on the Roman Empire, to make them more alien and fearsome.
This scenario forms the backstory of Gears of War. Sera's human population had been fighting each other for seventy-nine years and only just come to an exhausted peace when a massive, well-equipped, highly-organized army—the Locust Horde—erupted from the ground in multiple areas simultaneously and brought their civilization to its knees.
Even earlier, this happened to the Locust themselves, with the arrival of Lambency. It was the mutation's virulence that lead to the Locust eventually declaring their underground home a lost cause and making war with humanity because waging a genocidal war against humanity so that they could relocate to the surface was deemed easier than holding the Hollow.
The Conqueror in The Last Remnant shows up out of nowhere with an army and starts capturing Remnants until the current world order recognises him as a ruler. As it turns out, this is a Humanity on Trial thing to see how humans are using the power of the Remnants. They fail.
In a Bodycount trailer an African militiaman is surprised by a skyscraper rising from the ground, with a large door opening. He promptly gets one-shotted by a laser from a guy in futuristic body armour.
In The Elder Scrolls V: Skyrim almost everyone is blindsided by the Dragons. The only ones who have any idea where they came from are the Graybeards, and that's only because their mentor is another Dragon.
First in Nightfall was the return of Abaddon, the fallen sixth god, and his Margonite followers. The other gods had gone to great lengths to render him an Un-Deity so much of the players' knowledge of Abaddon is learned while on the run from his various armies.
Second in Eye of the North was the appearance of the Destroyers. While foreshadowed in an obscure Dwarven prophecy, nobody really knew about them until they were already halfway through slaughtering the Asurans. Even by the end of the campaign and their destruction very little was actually known about the Destroyers beyond that they were an enemy.
Third in the sequel, Guild Wars 2, is the appearance of the Elder Dragons. While they have been present since long before man or god walked the land, they were largely dormant and only hints of their power were seen.
Chakravartin in Asura's Wrath is a classic example. Absolutely no-one in the story had any inkling what his plans were, or that he even existed, until he straight-up manifested in the world and told the main characters. As the Supreme Being, his powers are infinitely greater than anybody else's. Asura beats him anyway.
One could say that The Black Baron from MadWorld fits. Granted he appears several times in the game, but did anyone expect to face him as the final boss?
To elaborate, the character in question has spent most of the game being killed in various ways to demonstrate the "Deathwatch Challenge" minigames. The player might expect to fight this character, but not as the final opponent. And it's a damn hard fight.
Gray Mann's Robotic Army in Team Fortress 2 managed to take everyone by surprise. What makes this notable is that Valve managed to sneak in references to this for almost two years before popping it on people.
The Grand Menaces from Sword of the Stars almost all have capabilities beyond the reckoning of the playable factionss. The System Killer is Exactly What It Says on the Tin in a universe where the lesser factions can only glass planet surfaces. The Puppetmaster can somehow subvert enemy ships and whole planets without recourse to lesser methods like Boarding Parties and ground invasion. The Locusts are Planet Looters that replicate exponentially if left unchecked. And those are just three of goodness knows how many. All will mop the floor with an unprepared player blindly going Attack! Attack! Attack! and are hard fights even with planning and strategy.
Medieval II Total War has two of these in the Grand Campaign. Unless you know it's coming and spend the entire early game preparing for it, the Mongol Hordes can steamroll any faction on the eastern half of the map, and even if you've prepared it's not going to be an easy fight. Then, about the time you think you've recovered from the Black Death towards the endgame, the Timurids show up, and on top of all the Mongols' strengths they have cannon-toting elephants.
The 3D Sonic the Hedgehog games generally use this as their source of villainy, as usual Big Bad Dr. Eggman's role is often demoted in these titles to either trying to benefit from the fact the villain is outside the typical context of the series or only rising to the level of being an instigator of the events and then loses his grip on them after some of the plot has passed. Examples include Chaos (a water monster from ancient times Eggman has been trying to harness but only ends up aiding its vengeful rampage) and Biolizard (a last-ditch experiment by a mad scientist aboard a space colony as his final parting gift for a world he believes betrayed him).
The Covenant were this for the UNSC in Halo. The UNSC is busy dealing with preventing a devastating civil war with their outer colonies, when suddenly a collective of alien races shows up, burns one of their planets to glass, and declares their intent to do the same to the rest of humanity. Despite this, the UNSC (while far from being on the winning side) adapts pretty quickly and lasts far longer than expected.
The Flood are this as well. While fighting aliens had become regular business for the UNSC, nobody expected space-zombies with a Hive Mind to enter the fray.
Massmouth 2 has the "Rattamahattas", a belligerent race which intends to conquer the hero's home planet and has no connection to the Big Bad of the game. They come out of nowhere, their attack fleet is soundly dealt with, then they are never brought up again.
The Saints are very much like the Doctor Who example; They're out of context heroes to the Zin. Zinyak never expected a gang of thugs from Earth to be able to take the fight to him so easily, and all his attempts to demoralize them and defeat them ended up backfiring. He did expect a few individuals to do some damage and had them under control, but otherwise the resistance came completely from left field.
BlazBlue is a series rife with Shinto and Norse symbolism, but the big reveal of Chronophantasma is that Izanami herself is the true Big Bad. Not a symbolically-named machine like the Susanooh unit, the actual Shinto goddess of the underworld is out to destroy everything.
Subverted in Homestuck in which any sort of villain that seems out of context has probably been foreshadowed at least once before. Namely, Her Imperious Condesce, a.k.a. Betty Crocker, who has appeared several times beforehand as John's greatest archenemy.
In a straight example, Bec Noir was this to the trolls. They had all but won their version of the game, when he came literally out of nowhere with no warning or context. In fact, it turns out that he came from the universe that they created by winning.
Even more so, Lord English, who destroys universes from the outside in.
The Old Ones in Cthulhu Slippers are this to humanity, and are so powerful they conquer earth in a night and a day. Like almost everything in the comic, it's Played for Laughs.
Frequently on WTFIWWY they would have a story about how a person (usually naked) would pretty much come out of nowhere. Usually it involves assualting people, acting crazy, or masturbating in public. Sometimes all three.
The Endbringers in Worm, massive, unstoppable monstrosities that regularly obliterate major population centers. Their origins and motivations are completely unknown though the characters theorize that someone is creating them.
ThunderCats (2011) presents Mumm-Ra this way to the Cats, as he and the Lost Technology his armies use have both been reduced to superstitions and legends in the centuries since he was first defeated by their ancestors.
Unicron in The Transformers series. Originally he was a terrifying Galactus Expy in The Movie before he was fleshed out as a god of chaos later on. Still, no-one had any idea how to deal with him in the first place when he showed up.
This was lampshaded in the original movie. Kup, the eldest of the surviving Autobots had at least one story for every occasion, usually a bad one. However, upon seeing the massive Unicron, all he could mutter was "nope, never seen anything like this before."
If there was one villain in My Little Pony: Friendship Is Magic that almost no one, in and out of universe, saw coming, it was The Changelings appearing at the very end of the second season. The only pony to know of their presence was trapped underneath Canterlot, imprisoned by the Changeling Queen and it's implied that she had no idea they existed until she was imprisoned in the first place. As for out of universe? Most theories for the finale didn't factor in shapeshifting insects, and the few that did guess something involving impersonation probably didn't think of something like that. Heck, the villain even used this to their advantage and struck at the best possible moment.