One of the actually popular cases is arguably Dark Link from the Water Temple in Ocarina of Time. In the middle of a, well, water-themed dungeon with water-themed enemies, you suddenly get a room that holds a Mind Screw and one of the most memorable bosses of the game.
Shiek's cryptic lines preceding the entrance to the Water Temple make reference to the use of water to 'reflect' upon one's inner self, so in a sense, the Dark Link battle could be seen as a metaphorical battle of the spirit connected to the idea of water. It still seems to come out of nowhere and is never referenced again.
Dark Link's original appearance as the Final Boss of Zelda II also may qualify, as Link already defeated the Temple Guardian. For some reason, a wizard draws out his shadow and they must fight.
Another clear example is Tentalus in Skyward Sword. Every prior dungeon boss had some story justification (Ghirahim was The Dragon, Moldarach was foreshadowed by Enemy Scans of the small scorpion enemies in the dungeon, Scaldera and Koloktos were objects in the dungeon enchanted by Ghirahim) but this giant tentacle-thing just inexplicably appears once you reach the boss room and tries to kill you and sink the Sandship for no reason. What makes this particularly egregious is that the Miniboss of said dungeon had a pretty strong plot connection to the place, being the Captain of the pirates who stole the ship in the first place.
At the end of Wind Waker, you march into Ganondorf's lair and prepare to fight him... he suddenly leaps up to the ceiling, and makes you fight several giant magical puppets modeled on bosses from previous games. Afterward, you have to laboriously climb up the puppet strings before you get to actually fight Ganondorf himself.
In Spider-Man vs. the Kingpin, Spider-Man fights a gorilla as a mini-boss while in Central Park looking for Sandman. Yes, a gorilla.
Most of the bosses in the console and PC tie-ins for the film are either from the film or villains from Spidey canon. The one exception is the boss Spidey fights when he infiltrates OsCorp, which is a Humongous Mecha with a Wave Motion Gun.
The video game The Matrix: Path of Neo more or less proceeded with the plot of the three Matrix movies. Until the very end, when instead all of the Smiths morphed into one giant "Mega-Smith" to fight Neo. Atari-esque avatars of the Wachowski Brothers stopped the plot at that point to explain how the metaphorical ending of the movies didn't translate well into a video game. This may be true, but it did feel like they were making fun of the player. ("Have fun... and enjoy enlightenment!" [Both laugh])
Despair Embodied from Devil May Cry 2. He pops out of the carcass of the previous boss without any prior in-plot mention of his existence.
Super Adventure Island II does this twice. The first one appears when you beat the giant bird hyped up as the final boss. Suddenly an evil wizard appears and steals Tina, and you have to play through the level again. When you kill the wizard, a giant space octopus appears, which is the real final boss. And you fight him in outer space for some inexplicable reason. There's some eerie music and mist filling the room when you kill the wizard, indicating the abrupt change in mood, which is nice, but you'd think the player deserves an explanation for this nonsense.
From the Ratchet & Clank series, there's the Warship (that's the only name it's given, and even then only if you leave and return) in the third game. It's a black gunship with a warp drive that shows up to make a platforming section on Daxx difficult, and is then fought as an actual boss. It's not mentioned in the dialogue (it doesn't even get a post-battle cut-scene), there's nothing else with its design or abilities in the game, and its destruction does nothing but open the path to the goal.
Similarly, there's the Mothership in the second game. Using Giant Clank to fight Thugs-4-Less' giant robots? Makes sense. Fighting a giant UFO that launches an army of respawning UFO-headed robots? Not so much.
The first boss of the first game qualifies too; it is never hinted at or mentioned before or after, and is pretty unexpected. While it seems to be the source of/related to similar, smaller enemies in the level, the character you meet after beating it doesn't mention it at all. The thing just kind of drops down from the ceiling.
Immediately after defeating the first final boss of Gungrave, an "Alien Head" erupts from the ground, causing you to fall from the previous boss's arena to an entirely separate corridor, in which you fight him for the true final battle. There is no dialogue to give you any clue as to what the hell just happened, and after defeating it, you are inexplicably placed outside the structure you're in. Much like the rest of the final level, the game neglected to mention many key details about this being, including his non-mutated human form. Which is a shame, since he actually plays an important role in the backstory, but you wouldn't know this if you had merely played the game.
Metal Slug 3's first four and a half levels are a fight against a human army (and the odd Giant Enemy Crab)... until you defeat the commander. At that point, an alien springs from his body, and the last half of the last level is a war against the invading aliens known as the Mars People.
The Mars People appeared first in Metal Slug 2, with small, small clues in the game before they showed up, so their appearance in part 3 isn't entirely unexpected. No, the real kicker was in Metal Slug 6, when different aliens show up out of nowhere and start eating the Mars People.
Sol Dae Rokker, the boss of mission four, supposedly "an artifact of the solar deity that some Japanese believe in". But again, some of the alternative routes of the game have you fighting acid-spewing snails, zombies, man-eating plants, titanic maggots, jellyfishes bigger than your submarine, and a squadron of the Japanese Army that isn't aware that World War II ended decades ago.
The Final Boss of Metal Slug 5 is another example of this trope. After fighting a terrorist cell for the whole game, your last opponent is... a giant demon.
Cave Story is solid for most of it (even the fight against a tiny superfast mushroom makes sense). Monster X and Ironhead, on the other hand, are literally out of nowhere. All the latter gives you is "Something's coming", and the former just suddenly tries to run you over once the boss music suddenly starts (and its dying cutscene is even more bizarre). Interestingly, Ironhead is pulled directly out ofone of the creator's earlier games. There's also Omega, which unlocks the sun stones in the Sand Zone, and Heavy Press nearly qualifies — however, after beating him, it's revealed that his Load-Bearing Boss nature is the only way to get to the final final FINAL final boss chamber.
A few times in Super Smash Bros. Brawl's Subspace Emissary. Most of the bosses only make sense in retrospect. Aside from being evil or disturbed, there's usually no real explanation. Case in point: Rayquaza attacking Diddy and Fox.
Parodied in Stinkoman 20X6. The boss of the Darius-style level — where all of the Mooks are generic sea-life or robots that resemble them — is described in the manual (which initially had no picture of it) as "a small and speedy octopus or squid." (It's actually a robot gangster.)
True Crime: Streets of LA has pretty much a whole chapter called House of Wu made of this trope. You went to investigate a Triad building. Then for no reason you fell down to the basement and fight zombies. The boss of the chapter is a huge Chinese dragon that breathes fire and swims around a lava pit. Since the game is a GTA-styled Wide Open Sandbox game with a standard cop-show material with no supernatural or weird stuff in it outside of that chapter, many consider it to be entirely out of place. The developers admitted this level was pretty much The Artifact of a prior build and apologized.
To a lesser extent, the fire-breathing opera boat from the sequel.
Klonoa 2: Dream Champ Tournament, as its title suggests, revolves around a tournament. However, the boss stages don't involve actually fighting the other competitors; instead, you have to race them, with your opponents acting like time limits and not otherwise showing up in the gameplay. The actual bosses of the game are just random creatures who appear on the track.
Ninja Gaiden II (2009) has one at the end of chapter seven. You've just finished dueling a boss who has a prominent part in the storyline, then the plane you are on crashes in the Arctic (or somewhere icy anyway) and a giant ankylosaurus made of molten rock appears out of the ground to fight you. To add insult to injury, when you defeat the boss, it will explode in what seems to be a cutscene... but is an actual explosion which will kill you if you're caught in it. And the only way to not die from the explosion is to hold the block button. This basically guarantees that players will die at least once from it.
It's actually a part of the ship, presumably the main core. However, you likely won't hear the references to it on the ship unless you have the subtitles turned on, and the scene of it emerging from the wrecked ship is so blink-and-you-miss-it quick that most players assume that it just came out of the ground. So, it still qualifies.
After you defeat the Big Bad in the arcade version of Astyanax, who is a Shout-Out to Emperor Palpatine from Star Wars, complete with "force lightning", you suddenly find yourself in the true final stage, which is a technorganic alien hive complete with eggs and facehuggers. At the end, of course is the "Queen Alien", which obviously looks like a Xenomorph from the Alien movies. Space Flea Hive Level From Nowhere?
The same thing happened in virtually every game in the Turrican series. The penultimate or final level would always be a Xenomorph hive straight out of Aliens, complete with face-huggers aplenty. Needless to say, Xenomorphs have nothing to do with the plot of any game of the series.
Castle Crashers also does this in the final level. As far as the bosses of The Very Definitely Final Dungeon go, although the Necromancer and Re-animated Cyclops were seen in the game previously, the burly painter with a lunchbox for a head who attacks by painting monsters that were ripped straight from Newgrounds was not.
Nor was the giant ear of corn in the Peasant village. Or the Sock Puppet Dragon (Meaning it was a dragon with a sock puppet). Or Medusa. Or the Ninja Pirates. Or the Saracen Beach Volleyball team... Pretty much every boss that didn't capture a princess came out of left field, really.
The Sega Mega Drive game Alien Soldieris this trope. Nearly every enemy (enemy in this case being equivalent to a boss in every other game) is unexplained save for a few, usually ungodly powerful, and progressively stranger (giant crabs in an airport for example). You cannot go longer than a minute or two without running into something giant, random, and unexplained.
The Guardian Legend's Final Boss, "It", appears out of nowhere in outer space after the Naju planetoid has been destroyed. Other out-of-place bosses are the "glider", which is actually an enemy from Zanac, and Teramute, a dragon that is only encountered in one corridor of the Forest area.
The final boss in the Castlevania: Dawn of Sorrow also qualifies, since no one expected it to burst out of Dmitri's body as a fusion of all the demons he dominated.
After all the strife and struggle of reaching the end of Castlevania Judgment, the player finally faces the mastermind behind the events of the game... The Time Reaper. Granted, he reveals that a villain from Kid Dracula, Galamoth, had sent him from TEN THOUSAND YEARS in the future to the past to alter history and make him replace Dracula as the Dark Lord, but, as a Youtube contender called Quarter Guy stated in his countdown video for his 15 favorite Castlevania bosses, there was no buildup to his identity other than he was messing with the timeline, and after he is defeated, he is never brought up again (Quarter Guy even considered it a Big Lipped Alligator Moment).
In Castlevania 64, you'll have to fight the demon salesman if you spend too much money on him. Technically an Optional Boss, but he comes out of nowhere demanding your soul in the final level, your hero makes no comment on the matter before or after the fight, and there's no gain from defeating him.
In Contra: Shattered Soldier, the True Final Boss, the Relic of Moirai, is one. Supposedly, he's some ancient Eldritch Abominationin a Can, and while it comes out of nowhere at the last second, the whole reason the aliens have been attacking Earth for years was because they are Jovians and we took the relic from them (and the shadowy conspiracy government covered it all up). They were just trying to get it back.
In Super C, the Final Boss is a weird techno-organic Giant Spider with a woman's face (nameless in the US version, but called Shadow Beast Kimkoh in Japan) that shoots small spiders at you. This enemy appears as a Mini-Boss in later games.
Metroid: Other M includes a bolt-from-the-blue Bonus Boss of the epilogue chapter, Phantoon. Why he's fought, how he's alive again after being defeated in Super Metroid, and what he had to do with anything on the Bottle Ship is never ever explained.
To be fair, though, the Scorpion is at least mentioned in a file before it arrived. How it got on the train is, of course, bizarre. But the real "say what?" boss is the Centurion Centipede, who comes out of a grate because it's a nice time for a boss fight with no previous mention.
Resident Evil 2 gives us a giant mutant crocodile that is fought in the sewers. It has no foreshadowing at all and due to the limitations of the Playstation graphics, the crocodile looks more like a normal croc that just grew huge. Resident Evil: The Darkside Chronicles gives the mutant croc a makeover and it looks more like a zombie crocodile, but it still retains no foreshadowing.
The Star Fox series loves this trope, particularly the 64 iteration. Nearly all of the level bosses just suddenly show up with little foreshadowing or dialogue to announce who or what they are until they actually appear.
Though the original SNES game has an alternate Final Boss that is arguably the greatest example in the series. After going through a secret level that made NO sense, you fight a Slot Machine that can only be beaten by getting Triple 7s on it.
Pretty much every single boss in Gunstar Heroes and its sequel embodies this trope. Case in point the board game level, which features a giant face named Melon Bread, a bunch of little slime men that swarm you and only have 1 HP each, a giant gumdrop that summons clones that explode for no reason, and a teddy bear that can be defeated by being run over by a car. I'd list more, but the sheer number alone would hurt my brain.
The final boss from Mega Man 2 would certainly count as this. Right as you reach the end of the caves underneath Wily Fortress, you meet up with Dr. Wily, expecting a battle against one of his mechas... But, for some reason, he literally levitates out of the Wily Saucer and transforms into what looks like some sort of space alien... Not only that, but the room becomes filled with stars and darkness, again without any prior lead-up. After you destroy this "true form" of Wily, it turns out to just be his Holograph Projector, and, as the room returns to normal, you see that Wily was just behind a console, operating the green-shooty-alien-holograph-thingie.
Yellow Devil in Mega Man 1 also counts. All the other opponents by far were obviously mechanical. You probably did not expect fight with a gelatinous cyclops thing.
Blues/Proto Man's first appearance in Mega Man 3 qualifies. He made sense later on, but that first time, he was just kinda... there.
There's also Doc Robot using the powers of the Robot Masters from Mega Man 2 after you beat the initial eight. There's no explanation for what he's even doing there in the first place, nor do we ever really get one.
Muramasa: The Demon Blade features a giant centipede attacking a building. Granted, it's actually a creature from the Japanese Mythology (the Oomukade if you want to know), but the story at that point indicated you were about to face off against a human antagonist instead.
In Dead Space, the bosses are usually given some sort of buildup; you find Doctor Mercer's notes on the creation of the Hunter before you actually fight it (And after you freeze it, Mercer will start to show up again shortly before the Hunter thaws), you spend an entire level trying to make a poison to kill the Leviathan but it doesn't work so you just have to shoot it a bunch of times, and the Hive Mind is alluded to several chapters prior to fighting it. However, the Slug is given zero foreshadowing. You get "Isaac, there's something blocking our communications" and have to man a giant gun in order to knock it off the antenna.
It only comes out of nowhere if while repairing the antenna you failed to look up at the giant grate that covers it and see all the necromorph flesh on the other side.
Dead Space 2 gives us The Tormenter which just sorta turns up after Isaac falls though the ceiling (Isaac had spent the last two and a half levels running from a human gunship).
In Prinny: Can I Really Be the Hero?, once you reach the Flavor Sage and everything suddenly seems to be going smoothly, the aforementioned Flavor Sage commands the random giant padlock behind him to turn into the Chefbot-9000 and attack the prinny in order to make the Ultra Dessert. The lead character even lampshades how incredibly random this is.
Prinny: Nine thousand?! Why does this thing even exist?!?!
Run Like Hell for the Xbox had a problem with this, where you will face off against Niles just after Nick sets reactor to explode and you face Niles, but after this awesome battle you face off against a weak spider-like member of the race as the last boss which is nowhere near as lethal or as bad as the last boss you faced, and he just sort of appears out of nowhere as if they weren't sure what to do for a final boss. To be fair, the series was ended on game one and it was intended to be a trilogy.
Pretty much every boss in Super Star Wars is a Giant Space Flea From Nowhere, including the Jawas' lava monster, a giant womp rat, and a mech in the Death Star.
Super Empire Strikes Back was somewhat good about bosses making sense (giant probe droids aside), but then Super Return of the Jedi includes a boss fight with EV 9 D 9 (Jabba's torture droid) in an Ewok Village, and a green fire-breathing tiger thing.
God of War 3 has you battling in various boss fights against gods, mythic characters, and even a Titan. After the last boss in the previous sentence, the next boss is... a giant scorpion who happens to live in the area you're exploring. True, it's hinted at by a newly appeared enemy type that hasn't been seen before and some notes on the ground in the area, and said boss is carrying an artifact you need to progress... but after all the epic previous battles, it seems a step down.
The Kirby franchise contains many of these, barring the recurring bosses, most notably Whispy Woods and Kracko, major characters, and whoever is the Big Bad, Bigger Bad, or Final Boss... usually. There are some bosses that can be called the Final Boss of the game (sub-game in Kirby Super Star and its remake) that come completely out of nowhere. Most notable are the Wham Bam Rock in Super Star's' The Great Cave Offensive, even more so in the remake when he gets special boss music, Miracle Matter in Kirby 64: The Crystal Shards, and Dark Nebula in Kirby Squeak Squad. Yes, the last of these explicitly has plot relevance, but very little.
A notable subversion in Kirby Super Star: The final bosses of Milky Way Wishes are this unless the player watched its introduction sequence. However, in the original Super Nintendo version of Kirby Super Star, the introduction sequence was both optional and not indicated to even exist, meaning many players probably wondered what was going on at the end of the game. This was corrected in the DS remake, where the introduction was automatically played.
The Rogons in Evo Search For Eden are a race of intelligent fish who are harming the whales, and the player is tasked with taking them down. Absolutely none of this is foreshadowed in any way, nor do the Rogons have any relevance to the rest of the game.
In the Japanese Famicom version of Star Wars, you run into Darth Vader a lot in the game. He shows up very early on, starting in the Sandcrawler for some reason. When you hit him, he turns into a scorpion. This actually happens throughout the game, and Darth Vader will transform into different creatures depending on the level. The real Darth Vader is actually fought twice.
In the relatively down-to-earth James Bond game Everything or Nothing, one of the early levels ends with Bond in a helicopter attacking a hidden base that rises out of the Nile that wouldn't look out of place in a Star Wars game. Never gets mentioned again.
At the end of Rainbow Six: Vegas 2, Bishop states that he/she must take down Gabriel Nowak him/herself, however, once the big showdown comes an attack chopper shows up instead of a one on one vs Nowak. It is completely unexpected in the sense that the whole game has you facing only human terrorists.
The PC game for Harry Potter and the Sorcerer's Stone has Harry escaping from the astronomy tower, pursued by Filch, to a Quiddtich game, and then randomly under the trap door — leading to the final battle with Voldemort. The game skips about half of the book and movie.
Treasures of the Deep has a level titled "Montezuma's Revenge", where you explore the underwater ruins of a Aztec Temple to find two pieces of Montezuma's lost treasure. After getting the first treasure, entering the room with the second brings you up close and personal with a giant reptilian monster with webbed underarms. The worst you faced up until this point were some angry crocodiles and booby traps.
Comic Jumper has Benny, a walking, talking Total Recall (1990) reference (complete with giant drill machine) show up in the last Silver Age level, followed by the giant photorealistic head of a Japanese kid in the first manga level.
Afro Samurai the game has a few of these. On the Bridge level the player finds themselves taking on several mini-bosses directly out of left field, with most of them immediately followed with an Indy Escape over a collapsing bridge. The first is an overconfident Big Mook who you later see mass-produced with a few standard mooks. The second is a band of 5 samurai aptly dubbed 'The Wild Five', who are troublesome but easily dealt with. And the last and most ludicrous is explosively introduced as Afro walks away from the fight with the Wild Five with no warning what-so-ever. A flying robot (that looks akin to FLCL's Canti) smashes through the bridge beneath Afro's feet and pulls him into the sky for a midair-freefall-boss-fight of Badass proportions. The player's navi guide in the shape of Afro Samurai's Ninja Ninja (Samuel L. Jackson) even presses the unexpectedness further by turning to the player (camera) and saying just how unexpected it was. "Did you just see that sh**?!... You go keep an eye on that fool, I'm gonna go get some coffee."
They are in Milla's mental world as well, she just keeps hers locked up in an out-of-the-way area.
Played straight and then lampshaded in Kid Icarus: Uprising. At the end of Chapter 8, Pit prepares to take on the captain of the Space Pirates in order to retrieve the three Sacred Treasures he used to defeat Medusa in the first game, when suddenly a giant Kraken leaps out of nowhere and eats him.
Palutena: "A Space Kraken?! Well that came out of nowhere!"
Halo: Reach's third mission, "Nightfall", has you fight a pair of giant reptilian space monkeys (no, not theBrutes) called Gútas from nowhere about halfway through. Originally, they were going to appear in more missions, but they ended up being cut from most of them except that level.
In Dead to Rights, at the end of the warehouse level, Jack Slate finds the guy he was chasing (Gopher) killed, and the person who killed him is... some random hulking dude with a crossbow called Longershoreman X who you then fight in a boss battle, this guy has zero build-up and there's no mention afterwards as to who he was or why he killed Gopher.
Metal Gear Rising: Revengeance has the Metal Gear EXCELSUS, piloted by Senator Armstrong. Even more-so is Armstrong himself, who afterwards bulks up and induces The Worf Effect upon Raiden. Even the Mission Control is shocked, since if you talk to Kevin beforehand, he'll note that there's nothing they dug up on Armstrong that could have suggested that he was in any form a physical threat (aside from the fact that he was in the Navy but didn't see any action).
As seen in the page quote, Trypticon from Transformers Convoy No Nazo isn't quite an example, but the game does still have an example in the form of a giant Decepticon logo that's fought more than once throughout the game.
In the second The Blair Witch Project game The Legend of Coffin Rock the final boss is something which looks like a cross between a lizard and a bull, and named "Schnell Geist". The only foreshadowing for this is one book in the library near the beginning of the game which describes a local folklore creature called "Snallygaster". Those are different names for the same thing, although the game never gives you that connection. It actually comes from real folklore for the Maryland region.
Final Fantasy III contains a prototype for these types of enemies in Cloud Of Darkness, a barely-explained cosmic force who pops quite literally out of nowhere to fight you after you beat Big Bad Xande.
Final Fantasy IV ups the ante with Zeromus, its final boss. He had only a vague connection to the plot, being the hatred of the main villain given form, and seemed to be present largely to provide a massive, intimidating final boss — which Zemus very much wasn't.
There's also Lugae. Halfway up a tower which you already know contains a boss you'll have to fight, you run into a guy in a lab coat with Einstein hair, who fights alongside an '80s Frankenstein's monster and then turns himself into a gangly zombie. And apparently survives both battles.
Ultros from Final Fantasy VI, the most amusing Space Flea ever. He's a giant purple octopus who comes out of nowhere and attacks you (in the Super Nintendo translation, he claimed to want to eat your party, which was at least some sort of motivation, but this wasn't in the original Japanese, nor the Game Boy Advance version, where he just attacks you and that's that). When you give him a beating, he escapes and later comes back to wreck the opera you're attending, along with other situations, for revenge. It's even funnier if you pick Gau and Cyan to go to the opera house. Why? Because this means your party is made up of members Ultros has never met before, and thus he's plotting "revenge" against a pack of total strangers.
He makes a cameo as a boss in The After Years, and the collective reaction of the party is something along the lines of "what the hell was that about?"
Atma/Ultima Weapon also fits this trope. He's the boss of the Disc One Final Dungeon, and enters battle delivering a Badass Boast about how ancient and powerful he is while a new, more foreboding boss theme begins to play. Aside from an off-hand mention from a single random NPC much earlier in the game, he's never mentioned beforehand and the party doesn't give him any thought afterward.
Siegfried/Ziegfried. He is a joke boss on the Phantom Train, also appearing in WoR Cave of Figaro and the Coliseum, who has no relevance to the story whatsoever. He is a "legendary" thief who has some relation to Ultros (this is not explained in detail), but despite being "legendary", the only two characters that mention him are himself and Ultros. It is probable that the version on the Phantom Train is actually an impostor, but this just adds to the randomness.
Arguably the most (in)famous example is Necron in Final Fantasy IX, predominantly because he is also a final boss who appears suddenly and has no prior lead-up within the context of the storyline. Fans have come up with many Epileptic Trees concerning his relevance and existence, but nothing definitive is ever provided, and his existence is not even mentioned during the ending sequence. Even worse, he directly followed Kuja, a legitimateBig Bad and one of the more popular villains in the series. One is left wondering if the designers wouldn't have been better off making Kuja a Sequential Boss.
Word of God says that Necron was a "thematic" final boss, acting to fight Zidane's desire to live with a being who represented total death (as opposed to Kuja, who was pretty much just deluded). The writers never even tried to tie him into the plot, though, stating he "could have" been several things. In the Japanese version, Necron's name is "The Eternal Darkness" when directly translated, making it clear that he isn't meant to be a character at all, but just a thematic force of nature.
Worth mentioning are two of the three main optional Mega Bosses (Kirin and the Pandemonium Warden, although the former's not so mega these days) who are thematically inappropriate with the areas they appear in (especially Kirin). Along with Absolute Virtue, there is dialogue indicating vague backgrounds with no real relevance to any of the game's overarching plots.
On a less-major level, several minor bosses throughout the series are just random monsters that turn up and fight you for no real reason, to ensure you are levelled properly.
The most infamous of those is probably FFVII's Schizo, a strange two-headed dragon who showed up immediately before another (actually plot relevant) boss fight, just to prove it wasn't even there for level structure reasons. It was just kinda there.
In Final Fantasy Mystic Quest, the Snow Crab, Jinn, and Medusa appear at the end of dungeons with no purpose except to give a boss fight. However, the Behemoth puts them to shame — it is fought at the start of the game and literally appears from nowhere, suddenly manifesting directly behind the player character and attacking them with no warning or reason.
Several bosses in Dissidia: Final Fantasy have no plot reasons for their encounter with the heroes, they just appear and decide to challenge you. The Warrior of Light's battles with Garland, Ultimecia and the Emperor are the most prevelant, he's searching for his Crystal, the enemy appears and taunts him, he replies Shut Up, Hannibal! and they fight.
Dragon Quest II had one of the earliest examples of the Giant Space Flea from Nowhere final boss. After defeating the Big Bad of the game, Sidoh (Malroth in the American version), who he turned out to serve and worship, appears out of nowhere to be the final boss. This was particularly nasty in the US version, as absolutely nothing hinted at his presence aside from a minor quest item named "Eye of Malroth", and he is infinitely harder than the game's Big Bad, Hargon, mostly because he randomly casts Healall to set his life back to full whenever he feels like it.
Dragon Quest in general is terrible about doing this to the final boss of the game. Even the very first one, the original text had the Dragonlord's pet superdragon come out of nowhere after you beat him (although the first translation changed this to his "true form" to help make the fight climactic and continuous.)
Deathtamoor of DQVI gets namedropped pretty late in the game, as well, with his evil being pretty much Offstage Villainy, via his minions.
Not that Dragon Quest VIII is without them, though. Megalodon and Ruin (from when you're trying to escape The Black Citadel) both fit this trope pretty well.
And VII is not without its Giant Space Fleas From Nowhere (although you're generally dealing with the effects of said Space Fleas); it's just that the (plot relevant) final boss is set up from the very beginning of the game. There are two Bonus Dungeons, with Bonus Bosses, but they're, well, bonus dungeons.
Dragon Quest V: Bjorn the Behemoose can appear to be one (emphasis on the Giant, he's the size of a mountain and is fought from the top of a tower) via accidental Sequence Breaking, as the key he drops is needed for the final dungeon but can be fought just after three-fourths of the way in the game.
Final Fantasy Adventure has the Metal Crab, Cyclops, and Golem which are all found in Mount Rocks. All three bosses are appear for no reason. Once defeated, they are never mentioned again.
Happens in the original Star Ocean, after a Fake Ending no less. Just when you think you've saved the day, all of a sudden, there's this Jie Revorse jackass to deal with, and there's absolutely no lead-up into this. The PSP rerelease at least has a minor rewrite in order to link him to the main plot.
The third game features literal Giant Space Fleas, literally from Nowhere, which invalidate entirely almost everything that happens previous to their arrival. Not a technical example of the trope since the entire second half of the game involves dealing with them, but considering the profound implications their arrival has on the entire series, the fact that they happen with absolutely no warning has gone so far as to break the base.
In SaGa Frontier, Emelia's final boss is an actual gigantic Mecha Shiva that drops down from the roof of the church where Emelia is pretending to have a wedding ceremony with the party in lieu of her dead boyfriend. Word of God explicitly states that there's no relationship at all between this creature and the Big Bad. It seems to exist solely to provide a final boss to the character arc.
Discussed in the elaborate Strategy Guide for the remakes of both Lunar games. The developers chose to remove several Giant Space Fleas that could distract from the main narrative. Of course, the remakes put a lot more emphasis on some of the baddies that did make sense.
Skies of Arcadia has quite a few of these. An overweight, acid-spewing rabbit, a giant robotic penguin with a death-ray, a floating tortoise that could make itself invincible, and a cockatrice-esque giant bird all appeared suddenly, were dispatched by the heroes, and died without comment from anyone.
There was a gigantic green blob in the game's sewer level (the aforementioned "acid-spewing rabbit"). What made him twice as bad was that not only does he come from nowhere, but after beating him, you immediately have to fight a boss that IS related to the story. That sequence sticks is one of the toughest parts of the entire game, partially because it happens so early and your healing options are very limited.
The Bleigock (the aforementioned "gigantic green blob") was likely there (placed by Valua, or more likely just because it was hungry) to eat the bodies that were dumped through the hole that Vyse is trying to enter the Coliseum through. The other mentioned creatures were bosses guarding the Moon Crystals (by coincidence or ancient design), which would be an understandable security measure to add.
Trunkle, a rock-tree-creature who suddenly appears at the end of the desert section to menace the princess for a distinctly nonspecific reason. If you go to that area before Peach is with you, Trunkle will be sleeping there; you can infer she woke him up and he got angry.
Robo Drilldigger for one. First you're chasing the soul of the Dream Stone... and then somehow it decides to try and kill you with a giant robot with drills for hands.
Mammoshka. You never know there's a powerful guardian on Mount Pajamaja unless you speak to one of the trapped Pi'illos on the mountain, otherwise you won't until you literally see it in the cut scene just before the fight. It's supposedly legendary... but no one ever mentions it except for said Pi'illo and the Massifs about 30 seconds before the battle.
Earthwake/Earth-waker. One minute you're walking through Dreamy Wakeport trying to free the Bedsmith from some Nightmare Orbs, next minute that Pi'illo Collector guy appears and warns you of a terrible guardian that attacks anyone who hits the nearby ! block (and you see a save block nearby). And even after hearing this, you most likely don't expect the building you're standing on to fly into the air, an alarm klaxon to sound and a Humongous Mecha made of buildings from the background to form and try to kill the Mario Bros.
Pi'illodium. You don't know about this ancient Pi'illo security system until it literally appears and someone asks what it is.
On the whole, Super Mario RPG: Legend of the Seven Stars is pretty good about making sure all its bosses are either connected to the plot in some way or at the very least foreshadowed. However, nothing whatsoever explains what happens when you break up the Princess's wedding to a minor villain: The chefs who prepared the wedding cake get upset that their work will be unappreciated, so they attack you. Then, the wedding cake inexplicably comes to life and uses its inexplicably vast magical powers to try and kill you for some inexplicable reason.
Punchinello from earlier in the game qualifies too. He has no lead-up, no one says anything about him, he's not one of the Big Bad's lackeys, and seems to have no reason to exist other than to make you fight someone for the third Star Piece. Punchinello badly wanted to be a feared supervillain, but nobody in the party knew who he was, and their asking him "who?" angers him so much that he attacks. His whole gag in the storyline is that he came from nowhere.
Boomer has little connection to the plot or role besides serving as a boss to fight before Exor.
Knife Guy and Grate Guy? Cloaker and Domino? Count Down? Mokura? The game's full of these elsewhere.
Smorg from Paper Mario: The Thousand-Year Door. While its individual components do cameo here and there throughout Chapter 6, it gave no indication that they would be able to amass together to create some giant animal made out of sentient balls of lint. The only apparent reason it exists is to give the chapter a boss fight that isn't Doopliss.
There are also the three giant Bloopers in the first Paper Mario. They serve no purpose in the game's story, and just appear without warning while you're exploring the sewers under Toad Town screaming "BLOOPER!" in huge text, and are not mentioned by anyone before or after fighting them. Although, by the time you see the Super Blooper (the third one), the shock has all but worn off.
There's also Kent C. Koopa, who you encounter on Pleasant Path. He literally shows up from out of nowhere to block your path for no good reason. You can either fight him or pay him a temporary toll, and it is absolutely necessary to use the path, so... (Actually there's a sign in the Mushroom Kingdom that foreshadows his existence. Make sure to read both sides of it each chapter).
Lampshaded in Suikoden, where encountering a random boss enemy that is not referenced before or after causes one character to exclaim something along the lines of "What the hell!?" before the fight. It's also played straight with a few other encounters.
Chernabog from Kingdom Hearts. He literally appears out of nowhere, after you've jumped through the hole in "The End of the World". You don't know who he is, Sora makes no comment about him whatsoever, it's never explained if he's a Heartless, what connection he's got to Xehanort or why he's even there, he's the only boss who doesn't get an entry in Jiminy Cricket's journal and he's never mentioned again. It's as though the developers just thought it would be a disservice not to include one of the most impressive Disney creations, even if they had to just drop it in without so much as a single word of context. It's just plain Rule of Cool (and copious Rule of Scary).
In his original appearance, Chernabog isn't really given a backstory either. The Night on Bald Mountain begins with him turning out to be the top of a mountain and proceeding to terrorize a nearby village in some pretty frightening scenes. Therefore, he could perhaps be considered a Giant Space Flea From Nowhere in Fantasia as well.
Chernabog is supposed to be Satan or the Devil. Think about that.
There's a brief reference to Bald Mountain... in Traverse Town. Which you may never actually notice. And which makes no actual reference to giant demons.
Apparently, when they were asked about him being in the game, the devs stated that Chernabog was originally going to be the final boss, as he was supposed to be the source of all of the Heartless. Unfortunately, having a Sephiroth proxy seemed cooler, so Ansem's battles were put in. That's why they're so relatively easy compared to his battle.
Note, that Chernabog apppears as Sora is traveling through the "Dark Paths" that the Heartless use to get from world to world. Each gate Sora travels is a different color depending on if that world's keyhole is locked or not; or if the Heartless never visited (Hundred Acre Woods). Chernabog's is red; implying this is a world that fell to darkness. Chernabog may just be the Heartless of an entire world.
The Granstream Saga produces a boss from nowhere. (But also manages to tie it into the plot while simultaneously nullifying the rest of the point of the game) You've happily completed the game's quest across four floating continents to save them from falling into the sea. (Then you're sucked into a black hole where someone named Demaar tells you that the whole world was an illusion and that you have to fight him to break a hundreds-of-years-long cycle.) To call it out of nowhere would be something of an understatement.
The Mud Imp and Son of Sun in Chrono Trigger. Giga Gaia seems like one, but it is evident it has something to do with guarding the Mountain of Woe.
What about that completely irrelevant almost random Evil From Another Dimension in Jade Empire when the protagonist is dead and trying to untaint Dirge? It and its minion explicitly state they're more or less completely irrelevant to the plot and that you will die now. Their in-game existance is purely so that you'll have one or two boss fights there at Dirge. It turned out to be the most disappointing Ancient Evil of Doom ever.
Nearly every boss in MOTHER 3. Notable ones include Master Eddy, an animate whirlpool you fight near Tanetane Island, and the Forlorn Junk Heap, a discarded clayman reinforced with scrap metal. Of course, considering what kind ofgame this is, you really can't complain about weirdness.
Chrono Cross and the Time Devourer. Sure, Lavos is mentioned a couple times in passing if you go out of your way to read side documents near the end. Schala isn't. But the game already gave two 'final' bosses before this, one at the end of a long dungeon and the prior requiring a long attunement and the entire game having built up to it. But then you fight this giant space-eating glowing thing that merged with Schala somehow and defeat it with The Power of Rock? What the hell? Dropping Magus in would have made about as much sense. Hell, Chrono, Marle, and a zombie Lucca would have made about as much sense. And what was with Miguel? Why was he a superpowered philosophical fisherman?
Most of the bosses in Chrono Cross fall into this category, really. Generally there's a thematic link between boss and area they're fought in, but pretty much any fight that's not preceded by a story scene exists solely to give the player another star level.
The roaming legendaries in Pokémon, once unlocked, can be found absolutely anywhere in the world and change location at random. You're just sitting there, training up your Golbat, when — HOLY CRAP! A RAIKOU!
The second generation actually did set up the (original) roaming legendaries of Raikou, Suicune, and Entei quite a bit. As far as their appearance in Generation III, or Latios, Latias, and (in Platinum) the bird trio? Or what Cresselia and Mespirit's deal is? Uh...
In the original games, Moltres also qualifies. His Ice and Lightning counterparts are found at the end of optional Ice and Lightning dungeonsnote Well, okay, Seafoam Rock isn't optional, but the area where Articuno's found is. Naturally, you'd expect find Moltres, the fire bird, in some kind of fire-themed area. Then you find him standing around in a dead end of the underground tunnel leading to the last bosses. He was relocated to a less bizarre area in the remakes.
The Final Boss of Rogue Galaxy is a very odd example of this. For the first two-thirds of the game, Valkog appeared to be the Big Bad; after a certain event (actually reaching Mariglenn/Eden), Valkog and his flunkies are suddenly demoted to Quirky Miniboss Squad and you don't expect to even SEE them again. However, once you face off against the supposed new Big Bad in a two-stage battle, Valkog shows up again...and through a convenient plot contrivance, he and his two flunkies and their spaceship are transformed into the Final Boss.
Ah, Ōkami... a long and winding story based on Eastern mythology and presented in a heavily stylized watercolor graphics evoking old Japanese prints. During the game, you battle shadow demons, multi-headed dragons, and Tengu to finally reach the final boss: A black whale-like fetus in a glass orb driving around a glowing technological ball-shaped mecha in the heart of a star ship. The idea may have been to give Yami a sense of wrongness compared to the rest of the world, but it still comes out of nowhere.
Erebus, the final boss of Persona 3: The Answer. It was mentioned in the first game that Nyx, the Big Bad, was being called into existence by the despair and depression of humanity, but the player was probably not expecting that those emotions would take the form of a giant, two-headed... thing made of shadow. For that matter, the main game's Big Bad was also kind of an example, being revealed after 80% of the game was over and never explained beyond wanting to bring about The End of the World as We Know It.
One could make the same case for Persona 4's True Final Boss, only she is revealed at the very last minute (as in moments before you're supposed to leave town on a bus.) This is made more apparent because the true murderer of the case you were trying to solve has already been defeated, as well as the being that was behind him. The plot also winds and swerves in so many directions that spoiling the True Final Boss by itself doesn't really give away anything else.
Of course, Persona 4's True Final Boss is the answer to the first question the player likely ever had. "Why do I suddenly have the power of Persona?" Thematically, that the player stopped caring after the first few minutes makes it the ultimate expression of the "Fog of Truth" — the question that cannot be seen.
In Dark Cloud 2 (Or Dark Chronicle), the final boss of the game, at the end of a bonus dungeon, is the Big Bad (for no reason) from the previous game.
Exists outside of time. It is the link between the games.
A lot of the bosses in Last Scenario. Some (generally the more human ones) at least merit some acknowledgment by the characters, but others (say, the Viviones) are never mentioned again, even if they took you a dozen tries to defeat.
Baten Kaitos Origins is particularly infamous for one of these. The game is a double disk, and you switch from one disk to the other right after battling a boss and moving to a new area. You have to save your progress when inserting the second disk, only to be shipwrecked and stranded in a hostile forest instantly and having to battle one of the most ridiculously difficult boss battles in the game (since, most likely than not, your party will be severely underleveled and the boss can heal itself). It ends up being one of the cheapest battles in the game, since it's completely unexpected and thus you'll be unprepared for it. And since you're stranded in a forest and you just saved your progress, you can't go back to raise your characters' level.
Baten Kaitos Lost Wings and the Eternal Ocean is similar. At one point you're in a ghostly area where it's stated that the walls between dimensions is weak. Best way to showcase this? A giant monster bursts out of another dimension, and you fight it back in.
The original .hack games were actually decent about its Giant Space Fleas. All the 8 Phases of Morgana may have looked bizarre — as BlackRose was oft to point out — but there was a point where that was expected. Even Cubia was given ample foreshadowing, although his initial appearance at the end of the first game certainly may have been a surprise.
The .hack//G.U. games each play out by introducing successive Space Fleas at the end of each game: the first game ended with a surprise AIDA infection after a battle with Tri-Edge actually, Azure Kite; the second game ended with Tri-Edge being revealed as the monster hiding in Ovan's arm, hitherto thought to be where Corbenik was hiding; then, suddenly, in the last game, Cubia appears.
Cubia was mentioned in the G.U. Terminal Disc that came with Rebirth. In a very usual hackish way, it had not been entirely forgotten.
Quite a few of the bosses in Eternal Sonata were these. Potentially justified, in that things don't always make sense in a dream.
Ultima III has one in the form of Exodus; not a traditional boss fight to end the game with, but instead, in the midst of a medieval fantasy setting: a computer into which you must insert four punchcards in the proper order. Not exactly what you were expecting, after the first two games, but paved the way for the last-boss-less sequels.
Armageddemon shows up in Digimon World 3 just before you get to fight the Big Bad. Every other Digimon boss is foreshadowed by having an overworld sprite; he doesn't. It's debatable whether he's supposed to be a boss — the random battle theme is used and it's possible to run from him. He's also one of three old bosses featured in the final boss battle.
He's used in a similar capacity in Digimon World DS, but this time he gets a line of dialogue and the player's character explaining what he is.
The main plot of Digimon World 3 also does this. All of the terror in the Digital World was supposedly caused by the MAGAMI company. However, after dispatching all of their head honchos, something called Lord Megadeath shows up and claims responsibility for everything. You are then transported to his orbiting satellite, where you fight him. Absolutely no mention of this character is made until just before that sequence.
The Big Bad of Anachronox is not revealed until the very endnote You can actually see him while on a trip to Sunder., his name is not revealed nor anything is known about him. It doesn't help that the game was supposed to have a sequel.
Baldur's Gate 2 had the Twisted Rune. Originally intended as the hidden cabal behind several sidequests, including the Athkatla slaver ring and the serial-killing tailor, the actual breadcrumb trail that was to lead to them ended up as cut content. They remained in, however, peacefully chilling in their evil clubhouse under the docks district unless the player randomly stumbled across the entrance, resulting in being dropped straight into a battle with an eclectic bunch of obscenely overpowered spellcasters after trying to enter an ordinary-looking house.
Interestingly enough, the previous game in the Golden Sun series, Golden Sun: The Lost Age, actually subverts this trope. At the end of the game, the main characters appear to be unhindered as they achieve their goal. Suddenly, the Wise One, a character that appeared very early on in the first game but was seemingly forgotten about until the very end, appears and summons a three-headed dragon to combat the characters. At this point, almost every playable character responds similarly to the player himself would at this point, pointing out that it's kind of odd that a being with god-like powers would do something as weird as summon a dragon to fight the protagonists, especially considering (which the characters actually point out), they've already defeated a two headed dragon in the last game. All the characters respond this way... except for token Wise old master Kraden. He realizes that nothing from a being called the Wise One could possibly be that simple, and, realizing that every major dragon they fought in the series was someone transformed, realizes that the three-headed dragon was actually the main characters' missing parents fused together. He tries to warn the characters, but is unable to before they defeat the dragon, fatally wounding their parents in the process. Whoops.
Brave Soul has two. One is a giant flying goldfish, although it gets a pass since it's found in some sunken ruins, and most of the monsters in the game look pretty weird anyway. The other, however, is a giant beetle, found in a Dragon's cave, and can't even be fought during the first visit, because of a scripted event triggered by the associated quest taking over control and moving the player directly to the destination. The only reason it was even included was because one of the developers already made it.
The third Darm Tower boss in Ys I and II, Khonsclard, is some weird spinning conglomeration of rocks. Many other bosses in the series also qualify, solely acting as beef gates or guarding plot coupons.
In The Elder Scrolls V: Skyrim, there's a quest for the Thieves' Guild where MavenBlack-Briar hires you to sabotage a competing meadery. The quest involves putting what amounts to rat poison into the Honningbrew Meadery's brew, and killing the skeevers (giant rats) that prompted the owner to hire an outside exterminator. Then you find an insane spell-slinging self-styled skeever master in the tunnels under the meadery. And he's not Squishy, and you have no clues that he even exists until the first Firebolt collides with your head.
It's arguable whether this counts. Yes, it's very much a "huh?" moment at the time, but his journal explains who he is and if you confront your contact about it, he tells you he knew about him. He still has no logical connection to the mission, though.
Grandia has this this in spades, not to mention you fight some of them again for no explained reason.
Dragon Age II has The Ancient Rock Wraith, the final boss of the first act. While there is a lore explanation for it (it's the spirit of a dwarf too evil to return to the Stone), it's only revealed after the battle.
In Metal Combat, after defeating the "real" Anubis (who seems to be either a robot or a particularly extensive cyborg), you fought Typhon and his/her ST, Giga-Desp.
The Strikers series (1945, 1945II, and 1945III/1999) lives on this trope. The attract screen and the PS1 version opening doesn't hint any Humongous Mecha forms of whatever boss fortress you face and an alien entity as the final bosses. Instead, the attract screens and intros show a WWII-themed shmup.
Aero Fighters has an alien entity — a giant skinless apeman — break off a jar as the final boss. The second game has you fight a black eyeball that resembles Buckbaird at the end, or a Bedsheet Ghost, which is randomly selected. Finally, at the third game, if you proceed good, you either fought a mutant ghost submarine in Bermuda Triangle, or go off to space and fight an UFO in another route. Do badly, and you'll fight a joke cartoon thing instead. And the rest of the game is you fighting various modern-day (sometimes future, however) war machines with a jetfighter (except the third). Oh, did I mention that you either go into space, a temple, or underwater in the final stages?
In Touhou, the EX stage of Lotus Land Story has Reimu and Marisa wandering through a dream world, uncertain how they even got there. Cue getting randomly jumped by the creator of that world in the guise of a Meido... and, once you've trounced her, her big sister shows up.
More generally, the early stage bosses are unlikely to have much to do with the plot, though the games seem to be moving away from this, as of the 12th and 13th games.
Lampshaded and inverted in Reimu's storyline in Lotus Land Story, where she pretty much only calls out and attacks the Stage 1 boss because she knows there's supposed to be a boss fight. Said boss was hiding from Reimu.
Jitterbug is built up as the Big Bad of Cave shooter Death Smiles. After you beat him, however, Tyrannosatan suddenly jumps out of an open portal to eat him. Tyrannosatan has no relevance to the plot, and is only there to provide a more climactic final boss. Although Jitterbug can come back as Bloody Jitterbug depending on how you've done.
Jitterbug may have attempted to summon Tyrannosatan, but since Evil Is Not a Toy, it eats him. Bloody Jitterbug may be the result of Jitterbug absorbing Tyrannosatan's power.
More likely, given Jitterbug's motivations to return to Earth, Tyrannosatan is the force behind the demonic invasion that came through said portal before him.
Since XOP has no real plot, most bosses are like this, but the final boss of the original is the most blatant. You've been fighting weird translucent aliens for the entire level, then you get the boss warning, and travel down some organic tentacled landscape, shooting blobs. Then you make it to an egg, it hatches...and a phoenix comes out and starts shooting lasers all over the place.
The ending of No More Heroes has got to be a parody of this, with a long stream of nonsensical boss fights and totally non-foreshadowed plot twists which push Travis to break the Fourth Wall and complain that the developers are just making this up as they go along.
The best example period is Mimmy from the second game. Travis has completed one of the toughest fights in the game and is now 7th, had a tense, sort of tough-to-watch scene, and suddenly this happens.
The classic X-Men arcade game inexplicably throws Nimrod (an advanced Sentinel from the future) at you. It doesn't make any sense why he would be working for Magneto, since he was designed to hunt and kill mutants. The same could be said of Wendigo, another boss in the game who has no connection with Magneto.
At the end of the second-to-last level, some pharaoh statues attack you in the tomb without any foreshadowing, and earlier on in the level, the players get attacked by six weak clones of Pyro.
As depicted above, Growl is all about beating to death hordes of poachers and freeing captive animals. When you take out their leader (a masked freak with enough strength to throw a tank), his corpse begins to slither around the arena, when suddenly a millipede bursts out of his back and states that it is the true leader of the poachers. (Players of the Darius games will recognize it as one of the aliens from those games, but there were barely any hints that Growl shared a universe with them.)
The arcade version of Double Dragon II: The Revenge took a turn to the occult for some of its enemy characters. The first boss, Burnov, is a masked wrestler who, instead of blinking into non-existence like all the other defeated enemies, will stand up and yell with his arms raised and then vanish into thin air, leaving behind his clothes and mask. In later encounters, he will rematerialize after using his death animation once. Later in the final stage, after defeating Machine Gun Willy, the game seems to be over until the player's own shadow starts gaining a life of its own and attacks the player as the actual final boss.
For most of Double Dragon 3, the player spent their time fighting human enemies such as bikers, martial artists, swordsmen and scantily-clad Roman warriors. In the fifth and final stage, the enemies consist of living tree people, stonemen and the reanimated corpse of Cleopatra(which in the NES version is a possessed Marion).
When The Simpsons got their own Beat 'em Up arcade game made by Konami, there was only the first season to draw material from. Thus, we got such surreal bosses as an unnamed professional wrestler, a Krusty The Clown parade float piloted by Mr. Smithers, two mobsters who copied the two-player combination attacks, a Cerny-esque fire-breathing giant hiding in Moe's Tavern, a bear, an anthropomorphic bowling ball conjured by Homer's imagination, and a Noh Theater actor with a Blade on a Stick.
Battle of Giants: Dinosaurs has Mystery Bosses, who are not super dinosaurs, but instead angry inanimate objects. They include monster trucks, rockets, telephone boxes, and a schoolhouse. It's jarring because otherwise you're in some kind of Land Before Time-esque world filled with dinosaurs, and no explanation is give for the phone boxes attacking you. On the other hand, seeing a T-Rex beat up a school is crazy awesome.
Akuma similarly comes from nowhere to face you in Puzzle Fighter (then again, the boss you were "supposed" to fight is Dan Hibiki).
Ditto for Akuma's first appearance as the True Final Boss in Super Street Fighter II Turbo, where he appears out of nowhere and kills M. Bison, who you normally fight. His name wasn't even shown then.
This happens again in Capcom Fighting Evolution. The game doesn't have a plot, yet it's still ridiculous seeing Shin Akuma suddenly showing up after defeating Pyron. Admittedly, you can only fight him after fulfilling specific requirements, but still...
If you said that Yami would be the boss of Tatsunoko vs. Capcom prior to its release, everyone would be mocking you.
Improved upon in Ultimate All-Stars, where some characters do in fact acknowledge 1) that Yami pulled their worlds together and 2) they had to beat it to undo said pulling.
The Touhou fighting game Touhou Hisoutensoku features three of them. One is Utsuho Reiuji, the final boss of Subterranean Animism. It's a bit of a stretch, though, as Sanae is descending into the geyser control center when you run into her, and if you're at all familiar with the story of Subterranean Animism, you probably expect to see her or at least someone else from that game. After you beat her, however, you fight Sanae's final boss, Suwako Moriya, who actually does come out of nowhere. Given that Suwako is already in the game as one of Sanae's assists (and you can even use Sanae's Suwako assist during the fight!), it's safe to say that no one was expecting her to be Sanae's final boss.
Who's the final boss of Guilty Gear Isuka? Is it Justice? Nope. Dizzy? Nope. That Man?!? Nope again. It's Leopaldon. Some strange, gigantic white beast with a huge puppy inside its mouth that is being controlled by a man in black who looks somewhat like the Black Mage.
The final boss in Tekken Tag Tournament is Unknown: a woman whose actions are controlled like a puppet by a forest spirit — which looks like a werewolf's torso — floating behind her. It probably helps that the game is non-canon, but she/they still come out of nowhere.
Tag Tournament 2 has Unknown return, but is less Space Flea-y, because the game confirms the Epileptic Trees floating around about it being Jun Kazama. Also, as a Continuity Nod to Unknown's own ending from the first, the wolf thingie is gone.
Samurai Shodown 6 is a "festival" game whose plot is basically that Yoshitora Tokugowa is holding a swordfighting tournament and will use his powers as "ruler of everything" to grant the winner one wish. The tournament gets hijacked by one of the four previous final bosses, then you go to HELL and fight Demon Haoh, right out of nowhere. Like the Tatsunoko vs. Capcom example above, neither the "hijacked" boss or Demon Haoh are ever mentioned again.
Master Hand in the original Super Smash Bros.. He's become a staple of the series, but in the first game you're going about your merry business fighting all these Nintendo characters, when all of a sudden you're deposited in a dark stage and MWA HA HA! this giant hand appears out of nowhere and starts attacking you! Sure, he was vaguely hinted at in the opening cutscene (where a mysterious hand picks up some figurines out of a toy chest and starts playing with them), but did anyone really expect to fight that hand? And to top it off, he's the only foe in the game that actually has Hit Points (normally the only way to die in the Smash universe is a Ring Out)...
Crazy Hand in Melee could be considered an even bigger case of this, as not only will he not even show up if you're not playing on a high enough difficulty, he also won't appear if you don't reach Master Hand fast enough, and even then, only appears after you damage him enough. His existence isn't hinted at in the slightest fashion, either.
By the same token, Giga Bowser in Melee's Adventure Mode. Just like Crazy Hand, he only shows up if you're playing on Normal or higher, within a certain amount of time, and without continuing. He returns as Bowser's Final Smash in Brawl.
Kil'jaeden, the Final Boss of the first World of Warcraft expansion, The Burning Crusade, could easily be considered one of these by players who aren't well versed in the background story of the game. It's not so much that he's an unknown entity (he's not), but that all of the marketing of Burning Crusade was focused exclusively on Illidan, the final boss of the Black Temple. Kil'jaeden, despite being one of the canonical Big Bads of the series, got almost no mention at all from the in-game story until suddenly being introduced in patch 2.4. Despite this, Sunwell Plateau (where you fight Kil'jaeden) is widely considered a Crowning Moment of Awesome in terms of dungeon design.
Blizzard has actually stated themselves that they released Black Temple too early and needed to find some way to keep everyone interested in the game. Still, it worked.
In Drak'Tharon Keep, the players fight a skeletal wind serpent named Tharon'ja. It's unclear whether this is supposed to be a spirit that the trolls worship, or a troll that ate its god like the trolls of Gundrak did.
Prince Malchezaar of Karazhan. The other bosses are mostly ghosts or magical constructs left behind in Medivh's castle, but while he's associated with the Eredar, it's never stated why he is there. The same applies to the nether dragon Netherspite.
Malchezaar is considered by Blizzard to be the last boss of Karazhan, effectively making him its ruler, as far as the unexplained storyline goes. The question of what does the Burning Legion want to do with a place like that is left for us to wonder.
More importantly, Karazhan is three unfinished dungeons (Well, one finished, two unfinished) combined into one.
A lot of minor dungeon bosses are this. They get one throw-away line to explain who they are and what they're doing. Sometimes.
In Cataclysm some effort has been made to explain some of the more bizarre bosses. New quests for classic dungeons offer some explanation of their background, though not every boss gets this.
Speaking of Cataclysm, let's not forget the final boss of the Worgen starting zone. Rather than using Crenshaw, the previously-introduced undead general that had bombed Gilneas City, Blizzard decided to put you and your friends up against a weird mutated orc named "The Machinist", who had never even been hinted at.
Guild Wars has one of these in Eye of the North, the Disc of Chaos. It has some of the highest health and damage seen on a mob and uses a model that has been flipped horizontally so it floats. The Disc only appears during its fight and is never mentioned before or after.
The Disc stands out even more due to its name. All other Destroyers have names in the format of "Destroyer of" or "of Destruction". The Disc is the only Destroyer to not follow this pattern.
Runescape has Chaos Elemental who, instead of residing in some sort of cave or building, is located in a seemingly uninteresting and generic spot in the Wilderness.
A few of the quests have boss battle creatures that come out of nowhere and have nothing to do with the story, just to make the quest a bit harder.
Lamp-shaded in the 'could you fetch my ball from the fenced yard' quest: the unnecessary boss morphs into six or seven arbitrary forms with escalating difficulty. Inverted in that earlier in the quest, you read the witch's journal where she mentions her experiment.
Averted in My Arm's Big Adenture. In this quest, you teach a troll how to farm. Once you have the stuff you need, My Arm (trolls are named for either the first thing they try to eat, or for the noise said thing makes; it was his father's arm) warns you about a "bird". Sure enough, once the goutweed is planted, a Giant Roc attacks you. If you're the type of player who ignores dialogue, you would have been caught by surprise. The mod who wrote the quest was probably counting on that.
As silly and nonsensical as Kingdom of Loathing is, the final boss takes it to a whole new level. Most other enemies in the game are parody versions of RPG monsters, which you kill with weapons and/or spells with goofy names. The final boss appears to be an evil sorceress, but she's actually a goddamn sausage. Literally, she's a sentient processed meat product. With ludicrously high HP and Reality Warper powers. It can only be defeated by using anagrams to deflect its attacks.
The boss of the Sandopolis Zone Act 1 from the Sonic the Hedgehog game Sonic and Knuckles. All of the other bosses in the game (and in fact most other Sonic games) are either Robotnik or his robotic henchmen. And then at the end of Sandopolis we get this big huge... golem thingy that you have to trick into the nearby quicksand pit. Yeah.
Actually referenced in Sonic Adventure 2 with the "Egg Golem" boss. Except that one was bigger, defeated in a different way, and was a robot.
King Boom Boo from Sonic Adventure 2 fits this trope perfectly. Seriously, Knuckles has to fight a giant bug-eyed ghost with a rainbow colored tongue for no reason? What was the point in even having this thing in? Did fighting the ghost even do anything to advance the plot?
Amusingly, the ghosts in that game are references to the aforementioned Sandopolis Zone.
The Leviathan boss in Gears of War 2 is essentially this, not being referenced at all in the storyline beyond some foreshadowing immediately before its arrival. It gets away with it by being awesome.
Punch-Out!! (Wii) has one when you get to fight a hidden boxer. Donkey Kong. Yes, the same Donkey Kong who beats up Kremlings and plays with Mario in sports and go-karting. He has no relation to the Punch Out franchise at all...unless you've played the old arcade version and seen The Cameo. See, sometimes there's a point!
You want to know what the original secret character was? Princess Peach. No joke.
Before that, some sort of sea monster attacks you in the sewer (if you play as Edward) or out of a rug (if you play as Aline).
Postal 2 was a semi-realistic game in that there were no "bosses" or monsters, just a free-roaming journey through a town inhabited by assorted screwed-up gun-toting humans with varying levels of craziness. Postal 2: Apocalypse Weekend ends with the sudden and completely out-of-left-field appearance of a "final boss" in the form of a 20-foot tall demonic half-cow half-man who declares "I am Mike J, Kosher Zombie Mad Cow, God of Hellfire! All bow down, and worship my asscock!". The Postal Dude promptly lampshades the trope by stating "Some designer has lost his tiny mind".
Win Back: Jin, the McNinja boss, is a blatant example. He is the only boss in the game to not have any introductory dialogue before the battle.
The final boss of Razing Storm is an enormous skull-shaped battleship. One of your comrades lampshades its sudden appearance by asking why no one told him about it, to which someone else responds, "Because we didn't know about it! Now keep firing!"
"Caduceus", the final boss of Strider 2, not only pops out of nowhere with no explanation or relevance to the plot, but is in fact gigantic, fought in outer space, and unmistakably flea-like.
Beyond The Beyond has Akkadias as the final boss, who is not mentioned anywhere prior in the entire game. The rest are all plot-relevant.
Spider-Man is a boss fight in Revenge of Shinobi. The only foreshadowing of this is a 'Copyright of Marvel Comics' at the beginning of the game.
Most Bosses from Blue Dragon don't really tie into even the countless sub-plots, and no one bats an eyelash after slaying them.
A Sachen game called Silent Assault had numerous bosses which even didn't make any sense. This is supposedly a game where aliens and mind-controlled humans are attacking the Earth, but bosses also consist of a floating skull, a computer with a mouth, a clown's head on a boot, a fire-breathing tree, and, as a final boss, a pair of sphinxes. However, it's Sachen so what do you expect.
Donkey Kong Jungle Beat features our simian hero fighting warthogs, other gorillas, and the occasional robot elephant. Then you get to the final boss fight, and meet: The Cactus King, a weird, green, giant space-gremlin with what looks like a dead tree for a head and rides a fire-breathing pig. Nothing in the game even hinted toward this character's existence, he has no motives, and totally clashes with the aesthetic featured in the rest of the game.
The Kalhar Boss Monster in Super Star Wars. Neither a King Mook (Mutant Womprat), nor a pet of the enemy (Jawenko), nor an Imperial guardian (Hover Combat Carrier), nor a monster from the movies (Sarlacc). Just appears out of the blue to block you from meeting Han Solo.
Not quite true. He is a monster from the movies... he's one of the pieces in the holographic chess game that Chewbacca plays with R 2 D 2. Doesn't make him showing up randomly at the cantina any less flea-like.
The almost forgotten SNK side shooter Prehistoric Isle in 1930 has the some of the usual Stock Dinosaurs as boss encounters, except the fourth one which is appropiately named "Unknown dinosaur": Part plant and part whale.
The ending to Borderlands. You're all geared up to fight Commandant Steele, whose mercenaries have been making your life difficult for the last quarter of the game, when suddenly a massive Eldritch Abomination pops out of the vault, impales Steele and swallows her whole, and then tries to kill the player.
Lampshaded in the intro of Borderlands 2, where Marcus states that the only things the Vault Hunters found were tentacles and disappointment.
In Fable, escaping a prison with your mother ends in a battle with a Kraken. What it's doing there or how it survives in what appears to be a pond of water just large enough to contain it is anyone's guess.
Sigma Star Saga gives us a few of these, including some literal giant space fleas from nowhere.
Indy platformer William And Sly has this with its final and only boss. Okay, it is mentioned in the beginning that something strange must be going on at the storehouse. But still...the game is an hour or so of relaxing platforming in the vein of Knytt. Impressive vistas, all exploration and scavenger-hunting, only a handful of not-very-threatening enemies. Then you top it off with an awkward and difficult fight against a giant phantom in the shape of a cobra's head.
Baron Brrr in Super Mario Galaxy (and also, to an extent the Undergrunt Gunner in many appearances). Baron Brrr has no lead in from the level to the boss other than being there, and unlike nearly every other boss, never appears again. Similarly, the Undergrunt Gunner, the very common cannon Monty Mole doesn't even get mentioned in the mission name, and appears in two levels completely out of the blue (and one, he's just guarding the cannon, right at the start of the level, and you don't even need to use said cannon.)
The Final Boss in Doom 64 is a giant space fly from nowhere, and a Subversion. It is alluded to only in the manual as what's been reviving and mutating the Demons for another invasion. The whole game and the collection of the three items for the superweapon are basically to stop this demon's resurrections from continuing.
In the game Sanitarium, after navigating a hedge maze, you have to face a scarecrow with a pumpkin for a head, wielding a scythe. The game may be based in the PC's subconscious mind, but this was a serious Level Breaker.
In Star Fox Adventures: Dinosaur Planet, the player gears up for a climactic showdown with the leader of the villainous dinosaurs, General Scales, when suddenly, out of nowhere, Andross shows up and reveals he's been behind everything, with no prior reference in the plot. Also a case of Hijacked by Ganon.
In addition, the Earth Walker Queen mentions how Scales has gotten stronger, and when Fox sees the transport holding Tricky, it's really high tech. Therefore it's implied early on that Scales may have been getting help from off world.
This seems to be an odd case, as even though there's no true indication to Andross's appearance at all, it ends up being a Rewatch Bonus. Playing the game again, you can notice the points where Andross may be talking to Fox, notably as the illusion of the Krazoa statue he appears from at the end of the game. It's also implied he's the one who trapped Krystal in the first place.
The international releases of the game using the "fight through an evil invading alien fleet" graphics from Salamander while putting the "fight through the body of a giant planet-eating alien" plot from the arcade version of Life Force (an Updated Re-release of the Salamander arcade game with redone graphics to match the plot change) in the manual didn't exactly help matters.
In Dawn of War: Winter Assault, there are two campaigns, Order (Imperial Guard and Eldar) and Disorder (Orks and Chaos). If you play the Disorder campaign before you play the order campaign you will be immensely surprised in mission five when Necrons, whom you had no knowledge of even being in this system, let alone coming to this planet, land and attack you. When you play the Order campaign it is explained by the Eldar characters that the Necrons are coming and why they want to attack. But if you play Disorder without playing Order first they seem like a Giant Space Flea From Nowhere.
This is always what forgotten beast attacks in Dwarf Fortress are. They attack with no warning, kill everything they find, and then promptly are killed or the fortress is wiped out.
In Master of Orion a Giant Space Amoeba From Nowhere will occasionally show up and charge across the map, killing everything in its path until it's destroyed. If you take it down, you get a significant boost to your standing with the other races.
In the sequel, it's a mild nuisance at best, unless you happen to encounter it at the start of the game, and it eats one of your planets, leaving behind a toxic rock. Due to the game's screwed-up terraforming mechanics (you can never improve toxic worlds, but you can turn a gas giant or an asteroids belt into a paradise), this planet is now nearly worthless to you.
Actually, toxic worlds can be improved — you just have to blow them up into asteroids first. This, in turn, requires giving the planet to an enemy before the game will let you target it with the planet-destroying weapon. Give to enemy -> blow up into asteroids -> convert asteroids to planet -> terraform newly non-toxic planet. Just make sure there's another planet in the system to do the "convert to planet" step from first.
A musical example: Elio e le Storie Tese's song "Supermassiccio" is actually about Giant Space Fleas from The Future that came out of a black hole. No, it's not supposed to make any sense.
Puyo Puyo Fever has an interesting case. It isn't the boss of the game that makes sense (no, it's just a big plot hole), but the secret boss; Carbuncle, who awards you for finding him with the hardest fight in the game series.
The final stage of the story mode of F-Zero GX. Most of the story involves Captain Falcon taking on Black Shadow and Deathborn, both of whom are introduced in the first cutscene. Nothing vastly out of the ordinary until the final stage, where, just as the story is being wrapped up, three ghosts representing the developers appear and announce that Deathborn was wrong about everything. They then challenge Captain Falcon to a race in a kind of digital dimension. He defeats them, they vanish, and the story just ends there.
In Dance Central 2, the entire career mode seems to hint that the Glitterati are the final boss. However, once you beat them, you're suddenly picked up by a passing airship, which reveals a mad scientist who wants to use his robots to replace all the dance crews in the city. Suddenly you have to do five dances in a row with hardly a break in between to beat them. And you have to get near-perfect scores for each one, or you lose. This boss is never even hinted at throughout the entire game until he suddenly appears to kidnap you.
Kingdom Rush: There you are, fending off bandits, orcs and other such enemies from attacking your castle, placing your newly acquired paladins and wizards here and there. Cue drone-shootingHumongous Mecha who beats the everloving crap out of your troops. The other two bosses aren't nearly as unexpected.