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When playing a higher difficulty in the Genesis version, you fight a 2nd form of Gedol. If you get all 7 hidden swords throughout the game, it becomes much easier, as his attacks in both forms will not do as much damage, and it also slightly influences the ending.
In Bomberman 64, a player who has gotten every Gold Card and "flawlessly" defeats Altair will get to see Sirius reveal himself as one of these, vaporize Altair with a Wave Motion Gun, and dare you to come after him.
Likewise, Bomberman 64 2: The Second Attack required you to collect the optional Light and Dark bombs to fight the Angel of Light and Shadow. Not only that but you must also fight a possessed Lilith halfway through the level rather than watch The goddess take control over her.
The arcade version of Golden Axe ends when you beat Death Adder. When you beat him in the Genesis version, it lets you think the game is over... and then cheerfully informs you that you have to fight Death Bringer now.
In NieR, the true final boss for Endings C and D is Kainé, who is unlocked in your third playthrough.
Clearing every Grudge Match in Custom RoboArena (which in turn requires beating the game and reaching 100% Completion) unlocks two more fights; a rematch against Eddy, and after that, a fight against Liv.
Contra: Shattered Soldier has two true final boss fights. The first, if you complete the first five missions with an A ranking, is a Sequential Boss fight with the "Relic of Moirai", then if you manage to achieve and maintain an S ranking through there, you get to fight his Very Definitely Final Form.
Neo also has two true final boss fights. Like Shattered Soldier, should you complete the first five missions with an A or S rank, the first one is a Sequential Boss battle with Master Contra. Beat him with an A or S rank, you'll fight him in his Very Definitely Final Form while falling through the Earth's atmosphere.
The Giant Space Flea from Nowhere final boss of ReBirth won't be fought unless you set the game's difficulty to Normal or above. It will appear after you complete Stage 5 on the above difficulties.
You also won't be able to fight Black Viper in 4 unless you play Normal or Hard.
Pokémon Rumble Blast has two. Beat the 5 EX levels and the EX 6 levels open up, where you respectively fight Mewtwo in EX Battle Royal 6 and Arceus in EX Team Battle 6.
This is a recurring trope in the Gundam Vs. games. In Gundam Vs. Zeta Gundam, if you reach a high enough ranking (RADM or higher), you'll go into an EX Stage. Depending on the route, you'll go up against high-tier mobile suits only who generally outnumber you, and in one particular has one of the openings from ZZ playing as the background music.
In the SEED-based games, getting a SEED ranking at the end of Arcade Mode nets you an extra solo battle against either Kira Yamato or Athrun Zala with all of their Gundams, their strongest ones being equipped with METEOR.
In Gundam Vs Gundam NEXT, clearing all of the EX Stages in an arcade playthrough (which requires enough points and generally not losing a battle) will unlock the NEXT FINAL stage where you go up against Kira yet again in a really suped up Strike Freedom with three separate phases (one as his normal self with a stupidly overpowered charged shot, the other being him in his METEOR and the last being the same as before but with infinite SEED factor).
Extreme Vs. Maxi Boost has an "Extra Final Scene" after fighting Sthesia Acht where you fight against a seemingly revived ex- (referred to as ex-(DC)) in the Extreme Gundam Mystic Phase from Full Boost.
In Mitsumete Knight, you get to fight the leader of the enemy army, Wolfgariothe Ravager, in his unmasked version if you have killed all the Generals who have appeared before him during the game. He's not more powerful than his masked version, but still follows this trope well, as his defeated animation in battle is different: instead of just dropping his sword and standing, contracted in pain, he now holds out his arm towards the sky, gets shocked by a thunderbolt, and falls on the ground.
If you play the Story Mode in Soulcalibur 3 normally, the final boss will be Abyss, but if you find the path to Olcadan and defeat him without ever continuing instead, you'll get the dreaded Night Terror as your final opponent.
Street Fighter IV moves it up a notch, having Akuma as a true final boss, then the harder to reach Gouken as the true true final boss.
Super Street Fighter IV turns them into their Shin forms, making them much harder. And the Arcade Edition adds Shin Evil Ryu and Shin Oni into the mix.
In Chapter 7 of Rival Schools, the player must defeat either Raizo or his brainwashed partner with a team-up combination attack in order to win the match. By doing this, the player will then be taken to the true final boss of the game, who happens to be Hyo Imawano, the nephew of Raizo and the true mastermind behind the game's story.
Both games of the Star Gladiator series use this particular very well. In Star Gladiator, the player must beat the game within a specific amount of time in Arcade Mode so that they can go on to fight the true final boss of the game, or else they'll get a false ending when they defeat Bilstein. In Plasma Sword, whether or not you get enough Battle Ability points from within Arcade Mode determines your character's ending. If they don't have the specific amount of Battle Ability points needed when you get to Stage 8, they get an abridged (false) ending, while defeating the eighth opponent and having the specific amount of Battle Ability points grants an extra special battle against each character's True Final Boss, which yields the extended, true conclusion of that person's storyline.
In the first Bushido Blade, to get the true final boss, you had to not get hit at all. There was a way to skip most of the opponents by running to a certain area of the map, take your opponent's legs out so they can't follow you, and jump down a well, which makes you fight only one more opponent before going onto the bosses. You still have to avoid getting hit to get the "real" ending for each character.
The flash game Amorphous+ sometimes surprises you with a Razor Queen instead of the annoying-as-fuck regular Queen. The game's normal "boss", the Queen, is nimble, has the ability to spawn other Queens (via a hostile takeover of another blob), carries two unbreakable claws to your one sword, is smart enough to avoid your swings, and can be beaten samurai style. The Razor Queen, on the other hand, is a colossal scorpion-looking thing with four huge claws that has an annoying penchant of turning you into Ludicrous Gibs. Beating her does unlock the Infinity+1 Sword (one of her claws), though there's not a lot you probably still need it for by this point.
The "Master Program" in Battle Circuit. You have to finish the game in one credit or get a high enough score.
Brawl parodies this, actually naming the second-to-last event match "The Final Battle" (versus Bowser, Ganondorf, and King Dedede) and the actual last match "The FINAL Final Battle" (versus Snake, Sonic, and a GIANT Mario). This trend continues in the Wii U game with its "Final Battle" being the same as Brawl's, and "The FINAL Final Battle" being against the company mascots Sonic, Mega Man, Pac-Man, and Mario.
In Melee, the second to last event is "Final Destination Match", which is a battle with Master Hand and Crazy Hand. The last match, "The Showdown", is a battle with Ganondorf, Mewtwo, and Giga Bowser (which Brawl's "FINAL Final Battle" is referencing, with the Giant Mario as Giga Bowser, and Snake and Sonic as Ganondorf and Mewtwo).
Also played straight in Melee and Brawl with Crazy Hand, who will only appear if the difficulty level is set high enough and certain other conditions are met. Melee's Adventure mode had similar conditions for fighting Giga Bowser. Beating him earns you a trophy and the sight of Bowser's Adventure Mode trophy actually falling into the abyss, then exploding into a million tiny fragments.
In Super Smash Bros. for Wii U and 3DS, landing enough hits on Master Hand or Crazy Hand on Intensity 5.1 or higher will cause Crazy Hand to flee, while Master Hand spasms and twists, clearly in pain as he transforms into the Master Core, a mass of shadow with five forms: Master Giant (a humanoid being), Master Beast (a scorpion-like being), Master Edges (an array of swords), Master Shadow (a Mirror Boss), and ultimately a defenseless orb, or on the higher Intensities in the Wii U version Master Fortress (a Womb Level). The number of forms that it uses varying depending on the difficulty, as only playing on Intensity 7.0 or higher will let you fight all of them.
Likewise, Art of Fighting 2 has a younger Geese Howard as a secret final boss under the same conditions.
In Fatal Fury 3, the player can only face the Jin Brothers if he has a high enough score after beating Yamazaki. If he makes it to Chonshu, then Chonrei appears if you had a grade of B or higher after beating Chonshu. Otherwise, the game gives the player a Bad End.
In Real Bout Special, if the player has a score of over 750,000 after beating Wolfgang Krauser, Geese Howard appears to challenge his character in a special "Nightmare" battle. If the player loses to him, it's a Game Over with no continues.
In Real Bout 2, get a high enough rank and/or beat Geese and Krauser without losing a round, and the player will fight... Alfred, the protagonist of Dominated Mind. Many consider him to be an Anti-Climax Boss, since his appearance is just a tie-in to a PS1 port of Real Bout Special that never left Japan.
In Mark of the Wolves, Kain R. Heinlein only appears if the player has a high enough grade after beating Grant.
The King of Fighters loves this one, too. Beating Krizalid with a high enough score in '99 let you fight Iori or Kyo, and in 2002 Unlimited Match, beating Krizalid, Clone Zero, Original Zero, or Igniz lets you fight Omega Rugal if you meet certain conditions. You only get one chance to beat him, and that is literally almost impossible unless you absolutely know what you're doing. Omega Rugal's stats are artificially increased to the point where one normal attack on them does roughly 1/3 of its normal damage. Basically, teamwork is key. Lose one set and it's Game Over. Win and you unlock them for regular play.
A variant of this existed in 97; when playing as the Hero team, if Kyo was the one that finished Orochi off, you'd go to a bonus battle with Iori.
In 2003, depending on how you defeat Kusanagi, you fight either Adelheid or Mukai.
And finally, XIII. If you get to the final team battle without enough points, the bad ending plays where it's hinted Saiki rewinds time and tries his initial Orochi resurrection plan again. Getting there with the right amount takes you to the final fights with Saiki and Dark Ash.
If you beat I-no in Guilty Gear XX Slash or Accent Core without continuing, and getting at least 10 Overdrive finishes, she creates a portal and transports you to the past, where you fight... Order Sol, an alternate version of Sol Badguy that wears Ky's jacket and doesn't use his trademark Fireseal sword. The character is available from the start, but the CPU Order-Sol is faster, stronger, and regenerates his exclusive charge meter. Not only that, he has an exclusive super move called Flame Distortion which is basically his normal Dragon Install on steroids. It regenerates his health faster than I-no, increases his power and speed even further, and gives him an unlimited super meter and charge meter. And it lasts for double the time of a normal Dragon Install (15 seconds). Oh, and you can't continue against him — lose and it's an automatic Game Over.
Dissidia 012 Final Fantasy, once you finish the 013 story mode and defeat Chaos, you unlock Confessions of the Creator, which reveals a side of the game's story previously only hinted at, and leads up to the combination True Final Boss and Bonus Boss, Feral Chaos. Defeating him unlocks the game's true ending as well as the ability to play as him.
Capcom vs. SNK 2. Upon the final match, certain requirements need to be met in order to fight the true final match, including score, getting the mid-boss before the final match (Bison or Geese), and accomplishing various ways to finish a match with a super combo. See StrategyWiki for full details. If you don't get the requirements, the game stops after the last team match. If you got enough, you fight either Akuma or Rugal chosen at random. Meeting the best requirements gives you Shin Akuma or God/Ultimate Rugal chosen at random.
Under ordinary circumstances, Battle Arena Toshinden ends with a generic "you win" message following the defeat of Gaia. But if the player makes it all the way past Gaia on Hard difficulty or above without losing a match, the battle with Gaia is followed by a battle with Sho, followed by a character-specific ending after Sho is defeated.
Digimon Battle Spirit has a partial example: Fulfilling certain conditions would cause Impmon to replace the Digimon you were supposed to fight beforehand, which acts as an SNK Boss (complete with power-nerfing as an unlockable). However, he doesn't entirely fit the trope because he's a midboss, not a final boss. The trope was more properly done in the Japan only expanded version. If you get to Milleniumon and beat him without losing once, it'll transform into ZeedMilleniumon.
In the PS2 version of Virtual-ON, if you beat all 8 mechs in under 15-25 seconds, you will fight the original version of Fei-Yen. This version of Fei-Yen is always in Hyper Mode, but with no downsides and increased stats.
SNK vs. Capcom: SVC Chaos has two true final bosses: A goddess version of Athena from the old Athena arcade game, and Red Arremer from Ghouls 'n Ghosts. Failing to meet them would give you a generic, text-only ending stating your character was never seen again.
And you only get one shot at these final bosses. If you lose, then your character gets transformed into something which varies depending on whether you fight Athena or Red Arremer before giving you the generic, text-only ending.
If you clear Arcade Mode in BlazBlue: Calamity Trigger with 10 or more Distortion Finishes and no rounds lost, you get the displeasure of fighting Unlimited Ragna, who has triple health and permanent Blood Kain.
And in the console versions of Continuum Shift, beating Hazama with the right amount of Astral Finishes and without losing a round rewards you with a fight against Mu-12. Unlimited Mu-12 that is. If you're using Mu in CS2 though, you fight Unlimited Ragna instead. If you're playing as Relius Clover in the Extend edition, you get to fight Unlimited Ragna as well. Hazama doesn't get a TFB.
In The Bouncer, you fight Dauragon three times. The first time, he ties a hand behind his back and still hits pretty hard. The second time is the final boss fight, and he's pretty tough. The third time, as the True Final Boss, he decides he doesn't need to hold back at all, and will easily pummel you with moves you haven't seen before.
There is even a fourth version of him where he is even more powerful, but you won't see this version until you have beaten the game three times though.
Touhou has two of these in its first Fighting Gameside storyImmaterial And Missing Power. With only two exceptions, each character's story mode lets you fight Yukari if you beat the previous five stages without continuing, and then lets you fight Suika if you don't continue against Yukari. (If you don't fight Yukari you get a bad ending, and if you beat Yukari but don't fight Suika, you get another bad ending). Naturally, the two characters without True Final Bosses are... Yukari and Suika.
After you get more and more information about what's going on in Duel Savior Destiny, the last route finally has you go up against God on his own turf, since he's responsible for everything (even if he didn't do anything directly). Otherwise, he'd just set events in motion again and try to destroy all of creation.
Shadow Jago (a Superpowered Evil Side of token hero Jago) in the 2013 Killer Instinct game appears only after you've earned all three of a character's endings and then beat the game with them on at least Medium and without losing, finishing the sixth match with an Ultra Combo.
Final Mix takes it a step further with the Secret Episode. This takes place during Aqua's time in the land of Darkness, where she fights off many pure-blood Heartless (such as Shadows, Neoshadows and Darkballs) until she faces a new unnamed boss Heartless. Also, this is the only time Heartless are fought in the game at all!
The Super Robot Wars games that feature "skill points" - optional challenges in each level - often have a harder final boss as a "reward" for completing most or all of them. Examples include Septuagint in Original Generation, Stern Regisseur in Original Generation 2, and the unholy powerful Neo Granzon in Alpha Gaiden.
Alpha 3 gives you the Final Boss of Alpha 2 as a friendly reinforcement. Note that the Alpha 3 reinforcement is full-powered. No Redemption Demotion degradation. Under the player's full control. It has more HP than anyone so far has bothered to try to find out, and is essentially unkillable.
Super Robot Wars W gives you the "true" ending on a second playthrough, including Critic piloting the true final boss, guarded by four copies of the previous final boss, and Applicant in the Val Arm showing up to help you.
Super Robot Wars Z2 has a variation — if you reach the final boss with enough Skill Points to be on Hard Mode, you are given the option to fight him at level 99 instead of his standard level 70.
Shin Super Robot Wars has the Devil Gundam piloted by Ghostelo in the La Vie En Rose as the true final boss if you beat the Earth and Space Routes and combine the data from both routes.
Shin Megami Tensei III: Nocturne had a fight like this against the Biggest Bad of them all, Lucifer. You have to complete the optional (and extremely hard) Labyrinth of Amala dungeon to fight him. Ironically, his entire justification for the fight is to prepare you for a war against an even biggerBig Bad: YHVH.
Megami Tensei II for the Famicom had, if you did everything right, YHVH Himself, in one of his only two appearances in the main series.
Overclocked, Devil Survivor'sUpdated Re-release, adds three new final bosses for the new 8th Days: Okuninushi, Japan's creator god in Amane's, Metatron, the Voice of God in Naoya's, and a souped-up Belberith in Yuzu's.
Persona 4 does this twice. At first, it looks like the final boss is Kunino-Sagiri, aka Taro Namatame. If you don't toss him into the TV, eventually you discover that the true final boss is resident bumbling detective Toru Adachi and a random godly entity called Ameno-Sagiri. But if you go to the Junes food court after saying your goodbyes, it turns out the true mastermind behind everything is the gas station attendant you met at the beginning of the game, aka Izanami. And yeah, you fight her at the end of the true final dungeon.
Star Force 3 just gets weird with this. As normal, getting every star lets you fight the super form of the final boss. However, inputting secret passwords lets you fight your Rival's new super form, and the super forms of the Bonus Boss, the Bonus Boss of the last game, and one of the new bosses. After all of that, you can fight the final boss's super SUPER form... as a random encounter. Not only that, but if you go through a long gauntlet of Wi-Fi matches (which is hard with all of the D Cers), you can fight yet another secret boss and earn a secret star.
In Fire Emblem Elibe: Sword of Seals, defeating Big Bad King Zephiel with all the gaiden chapters completed and all legendary weapons intact unlocks a few extra chapters, pitting you against The Remnant and culminating in the real final boss fight with Zephiel's literal Dragon, still under orders to carry out his ultimate plan.
Path of Radiance has something of an anticlimactic final boss on Easy and Normal mode, but he springs a cruel surprise on Hard mode: not only does he start moving (with a massive movement range of 10 spaces), after you "beat" him, he immediately invokes a dark god and resurrects with wildly increased stats and fully-replenished (and jacked-up) HP. And it's still your turn, meaning any units that attacked him are unable to act until your next turn! Adding to that, maybe five characters can actually inflict damage on him before he resurrects. (Eagle-eyed players might suspect something is amiss going into the final chapter, as there are less enemies on the map than in Normal mode.)
Similarly in Final Fantasy VII, Safer Sephiroth's HP depends on a variety of things, increasing 30,000 HP for each character at level 99, and increasing 80,000 HP if you cast Knights of the Round on JENOVA.Synthesis. Fortunately, his health is also decreased slightly for every time you killed the head while fighting Bizarro Sephiroth. Ultimately, his health, normally 80,000 HP, can range from 55,100 to 400,000.
In Pokémon Gold and Silver (and the Remakes), Red, the main character from the previous games, becomes this. You only meet him after getting all the Kanto badges (which only become available after beating the normal final boss) and going to Mt. Silver. After you defeat him, you get the second "ending", and the credits roll. Notably, in the HG/SS versions, he has the highest-levelled Pokemon of any trainer in the franchise.
In the fifth-gen games, when you fight the League after beating it once they face you with a full Pokémon team (as opposed to 4), more type and move variety, and a couple dozen levels higher, ultimately allowing you to properly face the Champion, Alder.
In Star Ocean: The Second Story, doing a seemingly totally random Private Action will release the "limiter" on the final boss, jacking up his stats and making him nigh-impossible to beat without ridiculous level grinding in the bonus dungeon.
Romancing SaGa: Minstrel's Song has an optional True Final Boss. If you manage to acquire all ten Fatestones (something that requires quite a bit of planning and cannot be accomplished until you have cleared the game at least twice), you can offer them all up to the final boss, vastly increasing his powers. The jump in strength for each stone beyond the fifth gets larger and larger, and the jump to the tenth is what makes 10FS Saruin a True Final Boss.
Disgaea 2 has a rare example of this (rare for the series anyway, which tends much more towards Bonus Bosses) if you go for the Worst Ending. Upon defeating Zenon, you end up fighting Rozalin/the real Overlord Zenon, who is at level 2000. (Compare with the previous fight with an enemy at level 90.) And unlike the other storyline fights with enemies at this level, you're supposed to win this one. Granted, it'll take a lot of grinding of a sort just to unlock this fight, but it can still catch you off guard. Luckily, there's a way to back out of qualifying for this ending. Which is a good thing, as your reward for victory is some Nightmare Fuel.
Disgaea 4 puts you up against against a different, much higher-leveled final boss if you clear the second to last stage using only the main character at level 500 or higher. You fight the messengers of God. Unfortunately, your reward is a Downer Ending.
In Record Of Agarest War, after spending how many hours in the game, you'd think Summeril is the Final Boss. If you unlocked the True Ending route (itself a Guide Dang It), you get to fight off against five sealed gods who are level 300 and the True Final Boss who is at level 350, when your level at this point is at most level 100.
Tales of Vesperia does a variation of this. Duke normally has two forms, however if you happen to have collected all of the Fell Arms in the game, he will resonate with them (for some reason), becoming the Radiant Winged One.
Dracula has a secret 3rd form in Castlevania: The Dracula X Chronicles that appears only if you rescue Annette (which means you have to save Iris and Terra. Saving Maria is not a requirement). After you beat the 2nd form again, he reverts to his original form and sprouts 6 demon butterfly wings and vanishes. He then proceeds to fire bats, fireballs, meteors, turn into a wolf, and use his own version of Richter's Hydro Storm. It's a lot harder than it sounds.
Considering that the Heavy Press is fought immediately before Ballos, it can be considered as part of the True Final Boss fight. This makes everything before the True Final Boss less stressful, but means the True Final Boss is five forms long.
A variation occurs in Metroid: Zero Mission. There's no extra boss, but if you collect 100% of items, the final boss will have roughly three times as much health as it normally does, and its attacks deal double damage.
In World of Warcraft, the Ulduar raid instance has an extra boss called Algalon the Observer that can only be fought after beating several other bosses in hard mode. Reportedly, he is far more difficult than Yogg-Saron (the normal final boss) and to make matters worse, will despawn if not beaten within an hour of the first try and won't come back until the instance resets.
Algalon the Raid Destroyer. He feeds on your tears.
As a boss, Yogg-Saron without any keepers was far harder before the recent onslaught of nerfs. Lore-wise, Algalon could wipe out Yogg-Saron and call it a day, but doesn't want to as it could destroy the world.
Another example happens in the Trial of the Crusader raid, where an NPC starts congratulating the players on completing the Trial... and is rudely interrupted.
In Cataclysm, Vanessa VanCleef from the Deadmines (Heroic mode only).
If you do Bastion of Twilight on normal mode, the final boss is Cho'gall, who was a fairly tough but doable boss. Beat his much more difficult encounter in heroic mode? The raid's not over, now you have to face the heroic-exclusive fight of Sinestra, a much more demanding fight.
In the Firelands, Ragnaros gains a fourth phase on Heroic, healing to half health and using entirely new mechanics.
Now there's another true final boss in Mists of Pandaria. After you defeat the Thunder King Lei Shen in heroic mode, you're then given the opportunity to fight a creation of the Titans named Ra-Den.
Kingdom of Loathing's final boss is normally the Naughty Sorceress, who has three forms. However, on some of the special challenge paths, her third form is interrupted by another enemy, such as the Guy Made Of Bees in "Bees Hate You", the Avatar of Sneaky Pete in "Avatar of Boris", and Rene C. Corman in "Zombie Master".
One fights one of two Elder Gods in the Bonus Dungeon "The Sea" depending on if you get to the Temple of the Underwater City through the Colosseum or the Library. If you collect each class's drop (so 12 fights) and then combine them, wear those, and enter the Temple immediately; instead you fight Dad Sea Monkee; or at least whatever he's channeling.
In Kirby 64 The Crystal Shards, not finishing the game with 100% Completion and thus the True Final Boss gets you a fake ending cutscene that is Nightmare Fuel to a lot of younger players: The fairy queen secretly smiling a pretty creepy Slasher Smile into the camera from behind her Scary Shiny Glasses, revealing that she's still being possessed by Zero. For many, this was the ultimate motivation to complete the game; everybody wanted to erase that creepy scene out of history. Once you do have all the Crystal Shards, you get to see the Crystal shoot a big beam of light at the fairy queen, driving Dark Matter out of her body. Dark Matter retreats to the center of the galaxy, and you chase after it and infiltrate it. After you get through the absurdly easy platforming bit, Dedede launches you into the air, and you fall through a void until Ribbon catches you. The Crystal turns into a gun, and a grotesque-looking cherub thing drops its disguise to reveal itself to be a resurrected Zero, hell-bent upon kicking your ass.
You also can not retreat from this battle. If you pause, your only options become the usual continue, and "TOUGH IT OUT!"
Kirby Superstar requires you to complete each of its modes, including mini-games, before revealing another mini-game in which you must Run the Gauntlet, defeating every enemy in the game in random sequence, keeping accumulated damage between battles.
In Ultra, there's the True Arena, a powered up version of the Arena unlocked after defeating the following semi bonus bosses. These are Wham Bam Jewel, Masked Dedede, and Galacta Knight. Here you will face powered up versions of some of the bosses as well as the three mentioned bosses. Once Galacta Knight is beaten, you'll see an epic cutscene showing Marx still alive floating in space and merging with the debris of Galactic Nova. He transforms into Marx Soul, a souped-up resurrected Marx, and you will fight him.
Similarly, Soul of Sectonia, the true final boss of Kirby Triple Deluxe is also fought in the True Arena. However, if you're only expecting a powered up version of the original boss fight, you're in for a surprise.
Ghosts N Goblins series always required you to play through the whole game twice (In one sitting) to get the right weapon to kill the Final Boss, but Ultimate Ghosts 'n' Goblins spiced things up by requiring you to find "magic rings", often hidden in impossible-to-reach places, to open the doors leading to Astaroth first and Hades later (the latter one requiring ALL of the 33 rings).
The spinoff series Gargoyles Quest had two of these in the third game, Demon's Crest for SNES. If you collected every crest and item, the final boss, Phalanx, would reveal a new form far more challenging than the previous ones. If you beat this and sat through the credits, you got a password unlocking an even harder final boss, Dark Demon, who could be defeated for a different ending.
In Super Mario 3D Land, the real final boss is Dry Bowser, who's fought at the end of Special World 8, although this battle is essentially just a harder version of the penultimate Bowser boss from World 8 and nowhere near as elaborate as the regular Final Boss. A much tougher final challenge lies tucked even further away into the post-game than this fight.
The Queen of Hearts in American Mc Gees Alice is relatively easy, if you know how to handle her. Her true form, on the other hand, is more difficult in comparison
Every 2D Sonic the Hedgehog game since Sonic & Knuckles has had an extra boss battle if you get all of the Emeralds. The main games usually open up a similar final boss battle by beating all of the branching storylines.
Inverted in Sonic the Fighters / Sonic Championship. Reaching round 2 of the penultimate boss fight without losing a single round will let you turn into Super Sonic, becoming invincible.
Sonic Heroes made you beat all four storylines and collect all seven Emeralds before you could face the final boss, Metal Sonic.
This gets particularly annoying in Shadow the Hedgehog, where there are ten endings that must be seen before the final stage opens up, some of which are pretty tough to reach unless you come through a certain penultimate stage.
And the trend continued with Sonic the Hedgehog (2006), where you must complete the three different storylines, each of which had their own different final bosses, to unlock the last episode where the three hedgehog heroes (after the worst level in the game) take on the ultimate final boss.
Played with in the 8-bit Sonic the Hedgehog 2, wherein beating the boss of Scrambled Egg Zone (Mecha Sonic/Silver Sonic) with all the Emeralds collected allowed the player to move on to the true final level, Crystal Egg Zone (which has the same amount of Acts as the others), fight the real final boss, and properly save Tails.
Sonic Adventure 2 only had two storylines to beat to open up the Last Story (compared to the six in Sonic Adventure, four in Sonic Heroes, and ten in Shadow the Hedgehog), but made up for it by having a super-long level (five parts, each using a different character) and a boss fight without the use of Super Mode before the obligatory Super Mode final fight.
Super Meat Boy has a second, much more difficult battle against Dr. Fetus once you beat most of the Dark World levels.
The Crash Bandicoot games usually avert this, at the worst making you fight the Final Boss two times, once without 100% Completion and once with it. The second GBA game plays it straight, though, where you need 100% completion to fight N. Tropy.
In Iji, after you have beaten the game once, you can use a switch to make the final boss much harder. This is literally done by activating the "make the boss harder" console accessible via teleport right before him. And the game even warns you.
Amazing Princess Sarahlampshades this trope after you beat the regular Final Boss by telling you that "You are not strong enough for the Greater Lilith." Beating the game unlocks one of six New Game+ modes that make the game harder, and after you beat all six, Lilith will assume her One-Winged Angel form and eat the regular final boss before challenging you herself.
Beating the entire story mode of Dr. Mario 64 in one sitting without continuing would pit you against Vampire Wario if you were Mario or Metal Mario if you were Wario. (Once you actually reached this point, you could continue and retry the match as many times as you liked.)
This only applies if you're playing on Normal or Hard difficulty. On Easy, you never get to see Metal Mario/Vampire Wario, regardless of whether or not you continue. In contrast, S-Hard difficulty subverts this by always pitting you against Metal Mario/Vampire Wario (the assumption being that if you're playing on S-Hard difficulty in the first place, you've already cleared story mode on Hard without continuing in order to earn the unlock code for S-Hard difficulty, meaning you already know about the existence of Metal Mario/Vampire Wario).
In most versions of Puyo Puyo Tsuu, racking up 180,000 points before reaching the final stage, without using any continues, replaces Satan with Masked Satan as the final boss. (The game challenges you to try this if you beat the game normally.) A special ending occurs if you can beat him, but frustratingly not in the Mega Drive version.
Tsuu also has a secret reverse example of this if you really go out of your way to suck. If you can manage to beat every opponent on the first floor without scoring enough points to advance to floor 2, you're pit against Masked Satan... and then get thrown out of the tower for sucking so hard. Video here. (Note that this is only possible in versions of Tsuu that require 30,000 points to advance to floor 2.)
In Fever, if you are playing Raffine's storyline, if you purposly lose 7 times, and defeat Ms. Accord without losing, the character who replaces Popoi is none other than Carbuncle! In fact, defeat Carbuncle and you will unlock him as a selectable character.
Also, in SUN, if you play the Hard mode, if you defeat every single stage without losing, Satan included, Carbuncle will battle you.
In PokémonPuzzle League, beating the game on any difficulty higher than Hard reveals that Gary wasn't the Puzzle Master. Rather, Mewtwo decided to use his psychic powers to be very good at this game. And if it's not enough that he's extremely difficult to beat him, you only get one shot to do so; if you lose to him, you won't be able to rematch him unless you beat Gary again.
Loco Roco 2: defeating the boss doesn't finish the game. After you clean up all of the dirt, an unlikely villain will pop up and result in a gameplay change.
If you take the right path in Meteos, you face off against True Meteo, which is really just three Meteos.
The Guitar Freaks and the Drum Mania series has a hidden and otherwise unreachable track for anyone who gets an "S" ranking on all of the three tracks he played normally.
The many Extra Stage songs of the BEMANI series (Dance Dance Revolution, beatmania IIDX, etc.) almost always require you to score a high enough grade on your last song (or all of your songs). Usually, these Extra Stages force you to play under modifiers that make the song even harder; for instance, Extra Stages in DDR force you to play with the x1.5 speed and Reverse mods, as well as a life meter that doesn't replenish. And in some of these games, this same requirement can be used to reach what is called the One More Extra Stage, or OMES for short; in DDR, this is a fairly easier song in which you fail instantly if you get one Good, Bad, Miss, or NG, and in beatmania IIDX, this is traditionally an even harder song.
In Pump It Up Exceed 2, if you get an 'S' ranking on both songs on Remix Station, you get to play a literally impossible song, RAW (which is also the opening theme). The steps, which include quintuple jumps and hitting all 10 panels at once, aren't meant to be played, but spell out a message.
DJMAX Technika 's Technical courses have you select three songs, do those songs, then face a boss song (that is not revealed until you get to it). However, clearing the first two stages with at least 95% of your hits being rated "MAX" will bring up an alternate fourth song. For example, the Customizer course's normal final boss is "Son of Sun," and the TFB is "Sin."
Pokemon Mystery Dungeon Rescue Team has Deoxys, who can only be fought once every single Pokemon in that game is fought and recruited (the final boss for Story Mode is Rayquaza). The true true final boss is Mewtwo, which can be battled after you obtain Ho-Oh.
Explorers have Darkrai, who set the plot of the entire game into motion. The player's amnesia and being turned into a Pokémon? His doing. Temporal Tower almost collapsing and Dialga's descent into insanity? His doing. Palkia trying to kill you? His doing! Not to mention, he planned a backup to everything, even the defeat at Dark Crater... although it failed to succeed, thanks to Palkia.
In Doom The Roguelike, nuking the Cyberdemon while under the effects of an Invulnerability Sphere will reveal the secret stairs to the next level, wherein resides the Ultimate Evil. It's John Carmack, and he has a rocket launcher and summons Barons of Hell.
This came out of an unintended feature in earlier versions of the game, where nuking the Cyberdemon still counted as a win, despite the fact you just killed yourself. In later versions, this was changed to marking it as a "partial" victory on your record, since you did technically commit suicide. Now, if you want to try to win that way and survive, the True Final Boss is there to make sure you're not just taking the cheap way out.
Mom is the final boss in the first playthrough. However, after that, two new levels are added with Mom's Heart as the final boss (True Final Boss). After the 9th playthrough, Mom's Heart is replaced with It Lives, a harder variation of Mom's Heart (Slightly Truer Final Boss).
The Halloween Update added a new final level that is normally unlocked after defeating It Lives, although there are a few ways to reach it earlier. At the end of the level, you fight Satan (Completely True Final Boss).
The Expansion Pack, Wrath of the Lamb, adds an alternate level after It Lives, with an Alternate Completely True Final Boss. It's Isaac (For a short time before being patched out, there even was an alternate boss to him, unlocked similarly to It Lives). And then after fulfilling another condition, you can go to yet another level after that one, where the Most Definitely True Final Boss lies: ???, Dead Baby.
Then there's the remake, Rebirth, which has three True Final Bosses. The first is the aforementioned ???/Dead Baby. The second is fought as ???'s counterpart, but after Satan instead. It's a being known as The Lamb. However, beating either of them unlocks the option to fight one last boss: the all powerful Mega Satan.
Shoot 'Em Up
Bullet Hell shooters take the cake for this, featuring impossible bosses such as Hibachi the mecha-bee from the DonPachi series. And to even reach them, you have to play their games with no continues.
Touhou has a few examples. In most cases, a level is not playable until certain conditions are met:
The second game, The Story of Eastern Wonderland, had a proper True Final Boss with Mima's second form (really third, but you don't fight the first one), which you can only see if you don't continue until then. Interestingly, you can continue at that form, but you get the bad ending.
In the fourth game, Lotus Land Story, the last stage and its Final Boss can only be reached if you play on a difficulty higher than easy, and you haven't continued until then. Otherwise, you receive the bad ending. The last stage also prevents you from continuing, period; there's no bad ending, it's just game over.
Similarly, the sixth game, Embodiment of Scarlet Devil, prevents the last stage from being played on Easy difficulty and sends you to the bad ending. If you play on Normal or higher, you can still reach the last stage even if you continue (and can continue on the last stage), but you still get the bad ending.
Finally for the shooting games, the eighth game, Imperishable Night, has an alternate final stage, with an alternate final boss, that you can only get to after beating the game once with the specific choice of characters. Continuing on the playthrough that unlocks the alternative final stage is fine, but continuing too much gets a Non-Standard Game Over ending. The true final stage itself can't be reached if you continue, and gives you the bad ending if you die on it.
It should be mentioned that the unlockable Extra Stages with their Extra Bosses are technically not this trope gameplay-wise, as unlike other examples, the Extra Stage is really selected from the title screen. Storyline-wise, it is debatable and depends on which game is being played.
It's also called the hardest video game boss ever, with good reason. There's even a video on Youtube by that name.
And thanks to the 360 port being region-free, anyone with a 360 can now experience it for themselves. What, can't even beat the first stage of Ultra? No problem, you can use Training mode to jump straight to the TFB!
Black Label's God Mode features an alternate form of the Final Boss, regarded by many players to be easier.
Hentai shooter Sentimental Shooting takes this one step further: Finish a stage (any stage) without using your time freeze and without losing a life, and a bonus boss would appear to blow you to smithereens. Level boss stages are the only exception to this rule.
DoDonPachi dai ou jou's Death Label mode pits you against not one Hibachi, but two of them. Have fun dying!
Hibachi's incarnation in DoDonPachi Dai Fukkatsu puts even Mushihime-sama Futari's TFB to shame.
And then Black Label Daifukkatsu added a new system that rapidly escalates the difficulty depending on how you play.
CAVE really outdid themselves in regards to this trope with Daifukkatsu Black Label, which introduces a second True Final Boss (provided certain requirements are met). Basically a literal Turns Red version of Hibachi.
Deathsmiles added one (Bloody Jitterbug) in Mega Black Label, which required you to access the final stage on rank 999 and not take damage up to Tyrranosatan. If that sounds a bit too easy, that's because the requirement for accessing Hades Castle at rank 999 includes beating both bonus stages... at rank 999. And the bonus stages have to be taken in a specific order, too, otherwise the rank will be back down to standard rank.
And in case you're wondering, yes, 1.1 arranged on the 360 version made it easier to reach him by making it only a 1cc requirement (no more ragequitting over getting hit, no more Rank 999, and no more forcing your way through The Gorge). Unfortunately, beating him this way does not unlock an achievement, as the relevant achievement specifically requires standard MBL.
Ray Crisis: If you manage to get to and beat the normal Final Boss, Dis-Human, without continuing, you reach the true final boss, Infinity.
Giga Wing normally ends after Stage 6 with a Bittersweet Ending in which your character self-destructs to destroy the Big Bad. Completing the first six stages without continues, however, takes you to the true final boss and secures you a better ending.
Ketsui Death Label has "DOOM Mode," which lets you fight the True Final Boss, Evacaneer DOOM (no relation) right off the bat. The catch is that you initially fight an easy version of it, and you fight it again and again, with the boss getting harder on subsequent rounds.
As implied, the original version also contains Evacaneer DOOM, but in order to see it, you need to beat the first loop of the game without dying or using bombs with a score of a certain cutoff.
Of course, this is still not as bad as Evacaneer DOOM in Death Label on Extra mode....yeah they upped him a BIT.
In Every Extend, Heavy mode has a different (replacement, not subsequent) final boss if you collect 7 quicken powerups and 800,000 points. This is doable but not particularly easy, although there's other ways to bring him in the area.
In Fraxy, it is possible to make a boss throw out a new form if the rank is 100!
In Rez, each of the first four areas has a Mega, Giga, and Tera version of the boss, depending on how well you did throughout the stage. The sudden shift in difficulty is a bit of a surprise the first time.
In Tyrian, this actually happens twice in a row; first, you fight a giant brain, after which everything is said to be over, BUT THEN! note yes, it's written like that in the game, the former Big Bad Vykromod appears as a giant nose. If you beat him, the game again states that everything is over, but if you found a certain secret earlier in the game, you now have to fight a minigame-like boss on the planet Soh Jin, which, if you win, is revealed to be a creation of Zinglon himself, who you then fight in an offscreen battle. In Episode V, it's revealed that Zinglon was behind Microsol and Vykromod in the first place.
My Little Pegasus: Kizuna DoPonyPachi has two. Normally, the game ends after defeating Angra Mainyu. If you're on the second loop, you then fight Enuma. On Ura loop, however, you fight a third boss, Caliburn, in addition to Enuma.
Starhall Redthel is very fond of these:
The final boss gets longer and longer on higher difficulties; it has one phase on Original mode, two on Hell mode, and three on Chaosside mode.
The thing the game actually calls the True Final Boss is this monster, which appears at the end if you have 14 or more lives and are playing on Hell mode or above.
There's yet another one, which requires a No Death Run. There's no video footage of it yet, but it completely puts the above to shame.
Cardinal Sins: Judgement Silversword Recycle Edition has the Mirror of Cardinal Sins, which requires the player to complete all seven stages with no F ranks. The Mirror also sports multiple forms, gaining more the better you performed in the preceding stages; there are four forms in all.
In Metal Gear Solid: Peace Walker, the true final boss will trigger upon completion of Metal Gear ZEKE and finishing all main ops. How difficult the boss fight is depends on how well you obtain the parts for ZEKE.
In Illbleed, there was a hidden final boss that could only be accessed in a New Game Plus, by purposfully not saving your kidnapped friends. Stranger still, every time you let one of them die, Eriko (the protagonist) loses her clothing, until she is eventually completely naked save for a tiny thong-like panty scrap and a couple of band-aids over her nipples. Reach the final arena like this, and instead of introducing the final boss, the announcer will start drooling over you and come down there himself. And believe it or not, it gets even stranger from there...
Resident Evil Outbreak has a final boss fight. Your characters run to escape only to be confronted by the boss you just defeated, again. You have the option of blowing him up with whatever weapons you have on hand or injecting him with the cure for the T-virus, which makes him explode.
Outbreak File #2 had this one boss follow you throughout the last leg of the finale scenario. Then, if you have to take the long way around to complete the scenario, the game fakes you out by making it seem like you have to fight him again, even if you killed him earlier. But another BOW absorbs him into its body and the True Final Boss fight begins!
Resident Evil 2 features two in the B Scenario. In the A Scenario, the last fight is against lion-like Birkin, who's tough, but still pretty easy to kill. In the B Scenario, you have to fight a heavily mutated Mr. X T-103 Tyrant, who's much faster than before, hits harder, and can only be defeated by the timely intervention of rocket-based explosives. Then, you reach the end of the story, only to find out that the A Scenario ended prematurely, and you have to fight Birkin one more time, plus he's mutated even further into a horrific vagina-esque blob. Only then will you see the real ending to the game.
The true enemy and ending in Parasite Eve can only be accessed by beating the game once, which unlocks the Chrysler Building. Reach the top floor and Aya will confront the Original Eve, possessing the "body" of Aya's deceased sister, Maya.
Fatal Frame 2 usually ends with a fight against "Rope Man" (aka the Kusabi). However, on Nightmare difficulty on the PS2 or Fatal difficulty on the Xbox, you fight Sae Kurosawa after him, and get a different, somewhat happier ending.
True Crime: Streets of LA had, based on player performance, story forks that led to worst to successively better endings and another Big Bad. Fortunately, each of these forks were well-written self-contained stories, and had their own unique features that made it worth it to explore each one, and doing so made the True Final Boss appear for the 100% Completion ending. It turns out to be the same boss as in the worst ending, but on steroids and crack.
Win Back plays with this by having you fight the true penultimate boss (Dan) before the normal final boss (Cecile).
In Star Wars: Rogue Squadron III: Rebel Strike, while not technically a boss, there is a bonus extension to one level if and only if you meet the requirements for a silver medal or higher. Earn a bronze medal and the level is finished and you win. Earn a silver or better and you play a short mission in a TIE Bomber and gain an opportunity to unlock said Bomber for use in other missions.
Ace Combat Zero plays with this. If you've beaten the game enough to unlock the SP Mission "The Gauntlet" on the highest difficulty, played that mission on said highest difficulty setting, and defeated Espada Squadron in less than 1 minute during the mission, then the game's penultimate boss Wizard Squadron appears. Do you have to fight them, too? Nope, instead a single F-22 Raptor appears from behind them and utterly slaughters Wizard Squadron in all of about 15 seconds. Then that F-22's pilot sets his sights on you. Good luck with Mobius 1, Cipher.
Air Force Delta Strike features NAVIGATOR on the final mission for 3rd Element. The only way to get to this boss is by using 3rd Element pilots for almost all of the space-based part of the game.
Warship Gunner 2 after the final boss has one where you have to sink a superweapon.
NavalOps: Warship Gunner does this on the second playthrough as well, but there is no mission break after sinking the Druna Skass, the Silfurbor Negla just sails right onto the level and starts shooting.
In Aerofighters Assault, you could only fight the actual final boss by clearing every mission, which includes the bonus ones, the game usually ending at "To be continued" after fighting Lars deep in the Antarctic. There are three in total, but the player will only usually get to play one in a normal playthrough. Getting to the other two requires both speed and a lot of points (which you'll usually net enough of by taking out the enemy jets). Once you get through this, you'll unlock the Space level with a final showdown against the series original final boss Pandora. While she has multiple forms, they're not based on damage levels like most bosses, but based on how much time has passed, starting as a UFO, then a flying weapon and at last her original form as a metallic golden skull with a dangling spinal cord. Luckily, you can just kill her before she even transforms by using FS-X's super attack.
NeoQuest, one of two online Neopets RPGs, features this, with an extra boss added for each difficulty. There are three levels to choose from: Normal, Hard, and InSaNe. On Normal, you'll only fight the standard Final Boss, Jahbal. On Hard, it's Jahbal, immediately followed by Mastermind. The ultimate battle consists of Jahbal, then Mastermind, then Xantan Reborn, a strengthened version of the first boss you fought, Xantan. You get no break between the three, and losing to Mastermind (or anyone, if you're playing on InSaNe) completely erases your save data. Have fun with that.
Infinity Blade has the God Kings. After you've played through the castle your first 15 or so times, you can actually buy the Infinity+1 Sword. This actually opens the doors to the four new immortal kings. The first three are really no problem, but the third is a Level 300 (the level cap in the game is 100 for players) robot mech with a man inside it. But you do get a sweet cinematic if you can best this insane challenge.
A driving/animal-catching game called Jambo! Safari had the goal was to catch (and presumably tag, not actually poach) wild animals on the African savannah. The last level was an all-or-nothing attempt to capture a saber-toothed tiger... unless you managed to get there in a single credit, in which case your final target was a white lion. The game's Attract Mode seemed to imply that if you somehow attained an even more perfect run, you'd have to catch a Moa.
In Tokyo Xtreme Racer: Drift 2, when you defeated Forever Knights, the Emotional King (final boss) in Hokkaido area of the game, you may think the story is finished. But no, Ground Zero is waiting for you in Hakone where you have started off, while it's stormy there.
Breakout clone Dark Ball 2 pulls this out in the most unexpected way. After beating Khross's second form, if you have the five secret kharma chips you get the Truth power up, which by this point seems to be there just to let you finish him off and avoid a bad ending. Then the ball reveals it was using you all along and was just interested in reaching this level of power, challenging you to the a fight to decide who will become a god.