The Bonus Boss is one that often exists outside the normal plot of the game, and requires quite a bit of conscious effort to get to. Its difficulty is usually much beyond that of the "story line" final boss. Occasionally, games may have more than one Bonus Boss. The key point here is that they make up the most difficult enemies in the game, and that includes the actual last boss of the game. Sometimes, the player may acquire an Infinity+1 Sword or ability once they beat this extraordinarily difficult enemy, but it's usually a Bragging Rights Reward. Anyone who can beat the Bonus Boss has proved they don't need them, unless it's to get to another Bonus Boss even harder than the previous one.
A Bonus Boss can technically be a Giant Space Flea from Nowhere, but then again, you went looking for it.
Compare True Final Boss, which is often (but not always) a Bonus Boss that, when found or unlocked, ends up replacing or coming right after the Final Boss, requiring you to beat it in order to clear the game.
A Bonus Boss that drops useful items may lead to Unstable Equilibrium. A Bonus Boss that is a boss from a previous game is a Legacy Boss Battle.
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The Four Sword Links in the The Legend of Zelda: A Link to the Past port on the Game Boy Advance. Each Link had some abilities that Link could use, such as the Hurricane Spin, the Magic Cape, etc. Beating them was purely for bragging rights.
The Updated Re-release of The Legend of Zelda: Link's Awakening for Game Boy Color featured a Bonus Dungeon based on color. The boss of the dungeon wasn't more difficult than the other bosses, but you could only enter the dungeon if you knew the color of the stalfos' clothes at the entrance. There were also a number of color-based puzzles that would be frustratingly difficult if you managed to get in anyway.
Castlevania: Order of Ecclesia gave you the option to fight the Chinese vampire, Jiang Shi, in the Large Cavern bonus dungeon. He's not very hard, though, seeing as how proper use of Melio Scutum and any slashing Glyph would easily reduce his 6000+ HP down to nothing. Though this boss is interesting in the fact that when he dies, a seal is placed on his face, but if you break it off with an attack, he comes back to life, allowing you to fight him again as many times as you want. Not worth the attribute points though (30, 60, or 120).
Galamoth in Castlevania: Symphony of the Night has more HP than Dracula and hits really, really hard. Fortunately, you don't have to beat him to meet the Count. Beezlebub is also optional, as are a few other bosses in the inverted castle.
The Whip's Memory, an image of Richter Belmont in Castlevania: Portrait of Ruin, is part of a ritual to unlock the true power of a weakened Vampire Killer whip. Unlike the rest of the game, you can only battle this boss with Jonathan. Thankfully, "dying" in this battle just boots you out of the battle with full HP and MP instead of yielding a Game Over.
Aquaria has a number of optional bosses, but many consider Simon Says to be the most interesting. He's well hidden, and you don't actually fight him — instead you play, well, simon says, with a very useful third cooking slot as your reward for playing well.
Metroid: Other M has the Metroid series's first bonus boss. If you play the post-credits sequence for 100% and the extra ending, you have to butt heads with Phantoon from Super Metroid, who not only has new powers, but is also much scarier looking than before. It is worth noting that the Phantoon fight was intentionally left out of Hard Mode.
Cave Story has G-CLONE, fightable in the removed Wind Fortress that was restored in the Steam and 3DS eShop versions as a bonus area.
Rodin from Bayonetta can be fought if the player buys a Platinum Ticket for 999,999 halos. He is revealed to be a former angel, and is more powerful than Jubileus. What? You say he just looks like Balder with a Scary Black Man makeover? Well, consider this: Balder didn't have WickedWeaves. Not only that, but regardless of what difficulty you've been playing on, the Rodin fight is automatically set to Nonstop Infinite Climax difficulty. He can kill you in two or three punches at the start of the fight. You want that Rodin weapon? If you don't know about the phone cheat, good luck.
In River City RansomBenny and Clyde are the only bosses that you don't have to defeat in order to access River City High School. Once inside, you can also skip Tex as well, since only Otis has to be defeated in order to fight the Dragon Twins, and then Slick, who is actually Simon.
Via Asura's Wrath DLC, two Bonus Bosses that have nothing to do with the main game story are Ryu and Akuma, who become Evil Ryu and Oni respectively.
The doujin game Grief Syndrome has Oktavia von Seckendorff, an optional sixth witch who can be fought at any point as long as Sayaka is dead. This already-difficult fight is made harder by the fact that you can't use Sayaka, who is generally considered the best character, against her — as anyone who's seen Puella Magi Madoka Magica to the end knows, Oktavia is the result of Sayaka becoming a witch.
the first game has Reptile as a secret boss. There is a very small chance that he will appear before the fight begins and give you clues on how to find him (ex."Look To La Luna"). You can only fight him if, on the fight at the Pit stage, you don't block, get a Double Flawless on your opponent, and finish them with a Fatality. Furthermore, there must be a ghost floating in front of the moon. If the conditions are met, the screen will flash with the words "You have found me, now prove yourself!" appearing, whereupon you will be taken to the Bottom of the Pit to fight him.
Mortal Kombat II continued the tradition with Noob Saibot, Jade, and Smoke. Noob Saibot appears only if you win 50 battles consecutively. Jade appears if, on the fight before the question-mark box, you only use the Low Kick button to defeat your opponent (can be done on any round). Smoke is the most difficult to get, as you have to make Dan Forden appear and say "TOASTY!" while fighting on the Portal stage, then hitting Down + Start while he's on the screen.
Mortal Kombat 3 had Smoke as a hidden boss via one of the 11 hidden treasures of Shao Kahn that you can access after beating the game, as well as Noob Saibot. Ultimate Mortal Kombat 3 added Mileena, Ermac, Classic Sub-Zero, and Human Smoke. Mortal Kombat Trilogy added Chameleon and Khameleon, who were basically all the male and female ninjas rolled into one, respectively. You can also fight every single one of these characters via the Kombat Kode system.
In Street Fighter Alpha 2 and Street Fighter III: 2nd Impact, each character has a specific rival who can only be fought if the player manages to fulfill certain conditions without losing a single match.
Baiken, in the original Guilty Gear for PS1. In order to get to her, you had to beat the game as Sol or Ky, without using any continues — once you get to her, though, you can try to win as many times as you like, and if you do, you unlock her as a playable character. Considering the extreme difficulty of defeating Justice the first time, and the first game's broken instant-kill mechanics, this was quite a task beyond the calling of most casual players.
Geese Howard in Real Bout Special. He dies in the first Real Bout, only to come back as "Nightmare Geese" in Real Bout Special (it's implied that the Nightmare Geese battle takes place in the player character's mind, as Geese has an odd aura around his feet and enhanced powers).
Melee has Giant Kirby, who appears in the fifth stage of Adventure Mode if the group of smaller Kirbies is beaten in 30 seconds or less. Giga Bowser also appears as a bonus boss if you clear Adventure Mode quickly enough; and while he fights exactly like Bowser, aside from being bigger and stronger, you can't grab Giga Bowser to throw him off the stage.
In Brawl, extra doors appear in three stages after you beat Tabuu; going inside them will pit you against Toon Link, Star Wolf, or Jigglypuff, depending on the level. However, you only have one chance to defeat them and their AI is much more aggressive than the characters you fought previously.
Soul Calibur 3 also has a bonus boss. The arcade and Tales Of Souls modes will almost always be fought against Zasalamel's demonic form, Abyss, but an even stronger opponent called Night Terror can be fought. Night Terror will replace Abyss if the player encounters and defeats Olcadan before arriving at the cathedral where the last few battles take place. Night Terror can also be fought in the 'Final Battle' mission of the game's challenge mode.
The sequel, Oratorio Tangram, has Ajim — a crystalline, transparent virtuaroid. To fight him, you must win at least one battle in your run with a Time Over. Once this is done, he will appear randomly at any time, even as late as the Raiden fight, crashing down on your opponent and destroying them. His stats are beyond mortal comprehension, meaning that he's faster and stronger than all other virtuaroids, and all damage done to it is lessened to roughly 5/8 of the usual. Oh, and you can't beat him via Time Over either — if you try and do this, you will lose automatically. Encountering him automatically unlocks him for regular play in the later revisions, but on the Dreamcast version 5.45, he was only playable by beating him, then beating the game, and holding both Turbo buttons on the Random select box on the latter half of each month. And when you play as him, he has the weakest armor in the game, and to make matters worse, his health drains by 2% every second.
FORCE, the 3rd installment, has Shadow versions of your team that you can fight by, once again, getting Time Overs. These Shadow mechs are manifestations of a virus in the system, taking the forms of your mechs and making them much stronger than the normal version. Jaguarandi also returns, but as the default mid-boss, and this time it becomes LUDICROUSLY HUGE, taking up over half of the arena. It's also a mutated Guarayakha now instead of a Raiden, trading in most of its long range advantages for godlike close range combat tactics. Ajim also appears, with a female version of it called Guerlain, but as the final boss, and utilizing completely different moves than before.
In the One Player story mode, there's Fire and Ice. To take on Fire, you need to be playing on at least the hardest non-hidden difficulty, beat your opponent on the Fire Pit arena, do a destruction on them, and enter a robot-specific code. If playing on the very hardest difficulty, beat Fire and do the destruction and code again and you can fight Ice. These two are extremely hard to beat, but the devs reward you generously for doing so. Normally, the end of round bonuses on the hardest difficulty are 400,000 points. For Fire, they're 2 million points, and for Ice they're 20 million points. Good luck getting a perfect round against Ice. The only way to not take any damage from him is to not take any hits at all, as he can still damage you even when blocking.
In the tournament mode, there are various unranked challengers in each tournament. All of them are hard, and most require you to be playing on the hardest difficulty. If they're going to show up, they'll challenge you after doing a destruction on some other opponent. There's at least one occasion when one unranked challenger will challenge you after beating another unranked challenger, too.
Blood Storm had several of these, all of them Palette Swaps of your main characters. Unlocking most of them was both fun and ridiculously frustrating. For example, one of them required you to knock down a stalactite in one stage using projectiles, so that it falls down a pit. Then, you have to jump down, land on the small platform, and then you'll be able to fight the boss. Another required you to drop your weapon, and then perform the "pick up" command so that you touch the center of a summoning circle. And so on.
The final boss of the story mode in Dissidia: Final Fantasy is Chaos, who is only level 50 or so and thus can be defeated easily with Level Grinding. However, beating him opens an extra campaign whose final boss is a level 110 Chaos called Ultimate Chaos.
Duodecim does the same thing, replacing the more-than-max-level Chaos with Chaos' new more-than-max-level One-Winged Angel, Feral Chaos. Your reward for beating him? The ability to play him.
Tekken 2 has Roger the kangaroo, who appears in the fourth stage if you beat the third stage with low enough health to get a "Great!" from the announcer. Beating him and the rest of Arcade Mode will unlock him and his Moveset Clone Alex, who is a dinosaur.
In Tekken 6, there's Nancy. She's basically one of several giant robots developed by the Mishima Zaibatsu, perhaps to combat Azazel, who is finally free after 10,000 years. Her appearance is sort of a Big Lipped Alligator Moment in that you get rewards for beating her but if you don't, it has absolutely no bearing on your progress and you don't get the option of fighting her again without restarting. She is playable, but only in one level of Scenario Campaign.
In BlazBlue the only way to fight Unlimited Ragna is to go through Score Attack Mode or to play through arcade mode finishing each opponent with a Distortion Drive.
Continuum Shift: Extend features "Abyss Mode", where a special version of Unlimited Ragna appears at Depth 666. The first thing you'll notice is that he'll already be across the screen in a few short frames, making him more annoying to fight than Taokaka in terms of speed.
In Persona 4 Arena, it's possible to unlock a special bonus match against Elizabeth, from Persona 3 (see below). She is an SNK Boss to the core, can inflict multiple status effects, can heal herself, and is insanely difficult to defeat. If she is in a position where she can win the match, she'll just perform her One-Hit Kill attack on you and be done with it.
Vampire Savior has Oboro Bishamon, the man himself, rather than the armor. Darkstalkers 3 makes him playable.
Borderlands has some in the optional side quests, some of which, like Mothrakk and Marley & Moe, can reach That One Boss status.
The trueBonus Boss doesn't come until you've downloaded and finished The Secret Armory of General Knoxx. That unlocks a fight against Crawmerax the Invincible, which is pretty much Exactly What It Says on the Tin. In case it's not clear, the game spells it out for you: the quest where you have to fight him is called "You. Will. Die." And the road leading to Crawmerax's lair features a road sign saying "Secret Final Boss".
Borderlands 2 keeps it up with a number of such enemies, with each DLC featuring a new Raid Boss:
Terramorphous The Invincible, who is even worse than Crawmerax. To quote a dev: "If you don't die at least 5 times before killing him, then we haven't done our jobs." The name of his quest? "You. Will. Die. (seriously)"
Some enemies can evolve in-game to turn into more powerful and resistant (and fully healed) versions of themselves. Most of these are still manageable. Let an Ultimate Badass Varkid evolve? You get Vernivorous The Invincible.
Hyperius the Invincible, a mutated, power-mad Hyperion engineer found in the Captain Scarlett and Her Pirate's Booty DLC.
Mister Torgue's Campaign of Carnage gives us Pete the Invincible — Pyro Pete isn't a very impressive boss when you fight him the first time, but when Moxxi says he's been working out since then, she means it.
Sir Hammerlock's Big Game Hunt has Voracidous the Invincible, who is aided by a powerful Witch Doctor who will buff Voracidous with his shields once killed.
Tiny Tina's Assault on Dragon Keep has The Ancient Dragons of Destruction, a Wolfpack Boss consisting of four dragons, two of which are capable of leveling up the other dragons and healing.
Hack and Slash
Diablo II has some in its later updates. Versions 1.00-1.09 had the Cow King as a sort of Bonus Boss, though he was substantially weaker than the actual final bosses. Version 1.10 introduced Uber Diablo as a new Bonus Boss, and 1.11 introduced the Pandemonium Quest, which involves looking for keys and battling buffed-up "Uber" versions of bosses (Uber Izual, Uber Duriel, and an important lore character Lilith, who is basically a "Uber" version of boss Andariel). The result of the quest is players entering the Uber Tristram, where they must fight an epic battle against Uber Baal, Uber Mephisto, and Pandemonium Diablo, the super versions of the three prime evils, who attack all at once!
Diablo III has the Infernal Machine update, which introduces four unique bosses, the key keepers, in each act. After obtaining all the keys, the player could craft the Infernal Machine, which allows battling two super-versions of game's bosses at once, for great rewards. There are three such battles: Maghda and the Skeleton King, Ghom and Rakanoth, Zoltun Kulle and the Siege Breaker Assault Beast. There is a special reward for winning all three battles and collecting special rare items from them.
Dungeon Siege has two. One is easy to find, while the second is extremely hard. The first is Scorch, the ancient dragon of Rathe, whom the player could avoid simply by continuing by the road to Castle Ehb. Scorch is the biggest monster in the game, has the highest number of HP, and is nearly as deadly as the final boss. The second Bonus Boss is located in the hard-to-find secret "Chicken level", amongst the various chickens named after the game's developers. It is Colonel Norick, the boss version of the first NPC quest giver in the main game, an old man who dies in front of the player. He also is a spoof on Colonel Sanders of KFC fame.
In the sequel to Otogi: Myth of Demons, the last bonus mission in the Forest of Havoc is a duel with The Crimson King, a recurring character from the first game. How hard is he? Let's list the ways. He hits like an angry truck, he can move just as fast as you, he throws magic fireballs that cause a bad status effect, and his ultimate attack hurts like hell... did I mention that it's a Homing Projectile? If you had trouble beating the last boss of the game, then The Crimson King will wreck you without mercy.
Most MMORPGs have such things: Giant Monsters in City of Heroes, world/raid bosses in Everquest, and raid bosses in World of Warcraft. Some are 'storyline' bosses, of course, but a lot of them are easily skippable.
Guild Wars features a few of them, most notably Urgoz, Kannaxi, Mallyx, Duncan the Black, and, most recently, Dhuum. To make matters worse, all of them (save for perhaps Duncan) have a hard dungeon to finish in one sitting before you can face them; if you die, you have to do it all over again! The placement of Mallyx and Duncan make them candidates for True Final Boss.
zOMG features the Landshark, which appears semi-randomly in Gold Beach. The Landshark is one of the only charge level 10 (max CL) monsters in the game, and features insane attack power, extremely high HP, and attacks that can take up almost the entire screen. If you see one, running is advised.
A recent update nerfed the Landshark to more manageable levels. (It's now only CL 7). However, a gamut of new bonus bosses were added in its stead, as well as "Challenge" versions of all Instance Bosses. While none of these (with the exception of Sea Witch and Labtech X) are CL 10, they have the added difficulty of only being vulnerable to individuals below a certain charge level. Meaning that players wishing to battle Airshark need to suppress their CL to level 2.
World of Warcraft also has its share of bonus bosses. The first one was Nightbane in Karazhan, where the only way to access him was to complete a certain quest chain. Wrath of the Lich King also introduced bonus bosses in some of the regular dungeons that are only accessible on Heroic difficulty. However, the WotLK bonus bosses tend to be much easier than the the Final Boss of their respective dungeons.
Just in case that isn't enough (likely, given how hardcore some fans of the game can be), many of these same bosses have special conditions that can be attained for Achievements (a Bragging Rights Reward, since you can't do anything with the points you accumulate from achievements), which often turn fairly normal bosses into insanity. For example, one of these takes place in a dungeon where there are minibosses that you can kill to make the main boss easier; for the achievements, you have to leave at least one of the minibosses alive until you engage the main boss. For the hardest achievement, all three get to stay up, and they come help the main boss while you're fighting him.
Yogg-Saron, the final boss of Ulduar, has a similar hard mode: you are required to defeat his four jailers, the Watchers (whom he's driven mad; defeating them restores their sanity) in order to open the path to Yogg's chamber. If you ask, they'll help you in the fight against Yogg-Saron. The achievements for defeating Yogg-Saron take the form "X Lights in the Darkness", where X is the number of jailers you ask to help you. Asking none of the jailers to help you is referred to as "Yogg+0", and is — even two updates later — the hardest fight in the game.
The Temple of Atal'Hakkar (aka Sunken Temple) has the first bonus boss in the game: The Avatar of Hakkar. You need to complete a quest chain to access him, too, and he's actually harder than the dungeon's final boss, Eranikus the Dreamer.
The best example, however, is Algalon the Observer (a.k.a. Algalon the Raid Destroyer) in the Ulduar raid. He is only accessible if you complete a quest that requires the player to kill several bosses in hard mode, and if he's not killed within an hour or so from summoning him, he'll despawn and you have to wait till the raid reset to summon him again. Algalon was not the hardest boss in the game when he was released — that honor went with Yogg-Saron on full hard mode (see above) — but he was the one that the fewest raids defeated, between the difficulty of the path to get to him and the difficulty of the fight itself. (As a special bonus, story-wise, if you fail to defeat Algalon, he sends a signal to his superiors to begin sterilizing the planet to rid it of corruption so that life can begin anew. Also, in-story, it's stated that he could completely and utterly wreck Yogg-Saron in a fight, and the main thing keeping him from actually doing so is that it would annihilate the universe.)
Jin'do the Hexer in Zul'Gurub was optional; you can actually skip him, and he drops some of the best loot in the dungeon next to Hakkar. Two other bosses were accessible through skill-related means; it was possible to fish up Gahr'zahka by catching fish to make a lure for him, and preparing a certain kind of mojo with Alchemy enabled raids to fight bosses at the Edge of Madness.
In the re-released Level 85 Heroic Zul'Gurub, people with enough Archaeology skill can access the optional boss at the Edge of Madness.
The Bug trio, Viscidus, and Ouro were all optional bosses in Temple of Ahn'Qiraj. Most, if not all guilds, did the Bug trio because the fight wasn't very difficult and it rewarded good loot. Viscidus is a fight that many guilds skipped because, even at level 80, it's still a pain in the ass. To defeat Viscidus, he must be frozen; naturally, he can only be frozen by Frost-based attacks, such as Mages' Frostbolt or Shamans' Frost Shock. Once Viscidus is frozen, then everyone in the raid must melee him (yes, even the healers need to). If melee'd enough times, he will shatter. All while attempting to freeze and shatter Viscidus, the raid must survive near-constant AoE Poison damage. Ouro is a fight that most Alliance guilds would skip in favor of C'Thun because A) he offered better loot and B) killing C'Thun at 60 was a significant achievement for raiding guilds. (Horde guilds would run him over due to Poison Cleansing Totem.)
A number of dungeons from Wrath of the Lich King have a boss that only appears when running the dungeon in Heroic mode. Eck in Gundrak is a good example, as not only does he only appear on heroic, but also appears in a side alcove that opens up after Moorabi is defeated on Heroic.
Recently introduced with the Cataclysm expansion is Lady Sinestra. Only accessible in 10 and 25 man raids, AFTER clearing the entirety of the Bastion of Twilight in Heroic mode.
In the Firelands, Ragnaros has an entirely new fourth phase on Heroic mode.
In Mists of Pandaria Patch 5.2, there is a bonus boss at the end of the Throne of Thunder raid, Ra-den. He is only accessible after you have defeated the previous 12 bosses. On heroic mode. Oh, and you know nothing about how to defeat him. Have fun!
You don't understand the math behind it, but you're pretty sure you're equal to or greater than eight of yourself.
Final Fantasy XI has the Notorious Monsters. The most, well, notorious of these are the Pandaemonium Warden, a Sequential Bosswith 10 different forms who has to be beaten in 2 hoursnote the time limit was instated after a group battled him for eighteen hours straight and still didn't win, and Absolute Virtue, who was originally designed as a Hopeless Boss Fight. Allegedly, they revamped him to be beatable, but other than exploiting bugs, nobody has yet beaten him. That's right: in an online game with over a million players, no group has even once managed to overcome Absolute Virtue.
He has now been beaten legitimately. It happened within two months of the Level Cap being raised to 80, but he is still nearly impossible.
He was beaten legitimately before by an alliance of Scholars stacking Modus Veritas, cue Modus Veritas getting a monster nerf to the point it's a waste of time and merits.
Kingdom of Loathing has the final bosses of the Clan Dungeons, and the three final bosses of The Sea.
Mother Slime in the Slime Tube, who can be up to level 8700. She can also gain immunities to elemental damage and is immune to stunning moves and items.
The Necbromancer in the Haunted Sorority House, who has three forms and a special attack that takes 30% of your HP.
Dreadsylvania has two possible bosses for each of the three zones: the Dreadsylvania Woods ends with either Falls-From-Sky, a bugbear made of stars that hits with a variety of powerful elemental attacks, or the Great Wolfof the Air, a hard-hitting winged werewolf; the Dreadsylvania Village has either Mayor Ghost, who randomly prevents you from dealing elemental damage, using spells or skills, or using combat items in the next round, or the Zombie Homeowner's Association, which is virtually immune to abilities that don't do extra damage to group monsters; finally, the Dreadsylvania Castle ends with either the Unkillable Skeleton, who scales to your stats, prevents use of combat items, and is only vulnerable to physical damage, or Count Drunkula, who takes drastically less damage unless your character is severely inebriated, and must be defeated in ten rounds.
The Sea, meanwhile, has bosses that are even tougher than the Clan Dungeon bosses, matched only by the Hard Mode Dreadsylvania bosses:
Shub-Jigguwat, Elder God of Violence, who saps all your MP (and some of your HP) at the start of combat, is immune to stuns, and is virtually immune to elemental damage. He will also retaliate fiercely if you hit him with anything but a basic attack.
Yog-Urt, Elder Goddess of Hatred, who sticks you with an effect that lasts about eight rounds, caps all your stats around 30, prevents you from using skills, does massive damage to you each round, and prevents you from attacking her on pain of death. She's also immune to stuns and won't let you use the same item twice in one combat.
Dad Sea Monkee, who can only be faced in the first place if you beat both of the first two Sea bosses as all six character classes, combine their special drops into six pieces of equipment, and wear them all. He's immune to being stunned, prevents you from using combat items, and is vulnerable to only one of the six types of damage each turn (including physical and all five elements). The order of those vulnerabilities is only vaguely hinted at in the cryptic, unsettling message you get before facing him. On top of all that, you have twelve rounds to defeat him before you lose the fight automatically.
Dragon Nest has several high level maps feature alternative routes with different bosses.
The Dreadful Entity. To summon the Entity at all, Dreadtooth, the world boss of Section X, must be defeated with full stacks of Dreadful Resurgence. The fight is quite a task, almost demanding a full operation's group. To add to it, Dreadtooth only gains stacks as he is defeated. Upon spawning, he starts with two. When he spawns again, he has four and so on. If Dreadtooth is defeated, he drops a special amulet which can be used to summon the Entity during the "Terror From Beyond" operation. But only in 16-player Hard Mode. To add to this, he has a special ability, Dread Touch, which is mitigated by another item: the Dread Guard's Corrupted Mask.
Upon Dreadful Entity's defeat, the Dreadful Entity drops an item called the Dreadful Orb. This is used to summon the second bonus boss - The Hateful Entity, in the Scum and Villiany operation on 16-player Nightmare Mode. Boasting the same abilities as Dreadful, but hitting much harder and requiring very specific kiting tactics to defeat, the sight of players with his unique title are rare indeed.
Mega Man X6 had some bonus bosses by going through alternate routes to fight Zero Nightmare, which nets you Zero, and High Max, which lets you skip straight to the last areas of the game, although it's hard to find out how the hell you're supposed to even damage him. (Hint: Stun him with a charge shot, then hit him with any special weapon.) Going to the secret areas again will let you fight Dynamo, which lets you get large amounts of souls.
X8 had Cut Man, again. You need to go through Optic Sunflower's stage to reach a 3D-ified version of where you fought him in Mega Man.
X3 had Vile MK-2, which does nothing when defeated, except when his weakness (Ray Splasher or Spinning Blade) is used to score the final hit, in which case you won't fight him later. This is only the first step in getting the Infinity+1 Sword. There was also Bit and Byte, who, like the X-Hunter example below, you could find and battle in hidden areas in stages. If you beat them using their weaknesses to score the final hit (Frost Shield or Triad Thunder for Bit and Tornado Fang or Ray Splasher for Byte), then they would be replaced in the final stage by Press Disposer. If even one of them was left alive, however, then the player would fight Godkarmachine O Inary in the final stage. Also, if Vile was defeated, the player would fight Volt Kurageil and Mosquitus in the final stage instead - defeating Mosquitus with Zero is the requirement for X to obtain the Z-Saber.
''X2 has the X-Hunters, Serges, Violen, and Agile, who can be encountered in hidden areas in stages. If you beat them at the first opportunity, you receive parts of Zero, and collecting all of them enables you to skip the fight with Zero in the final stage. You still fight the X-Hunters in the final stages, regardless of whether you fought them before or not, though.
Proto Man in Mega Man 7, who can be fought in a secret area in Shade Man's level after meeting certain requirements. The reward is his shield.
Mega Man 8 had two in the Sega Saturn version, and they happen to be Cut Man and Wood Man from Mega Man 1 and 2, respectively. Unlike their original appearance, however, they only give you bolts to buy weapons with. Cut Man is hidden in Duo's stage halfway through the game. Wood Man doesn't play the trope straight, though, as you fight him right before the continue point in Search Man's stage.
Fan game Mega Man Unlimited has Yoku Man. You unlock his stage by collecting 4 letters hidden in alternate paths of four of the eight Robot Master stages, and killing him gives you the Yoku Attack, which is a homing attack that can also be used to grab out-of-reach items and also kill Yoku Man in two hits in the Boss Rush later on.
In Mega Man ZX, after beating the penultimate stage, a new area behind it opens up. Inside, past a path lined with the familiar disappearing blocks and spikes, you can find Omega Zero, from the last battle in Zero 3, complete with famous quote. This battle is noteworthy for actually being HARD, not just "OMG he's level 500", since this time your character has far fewer abilities. Omega's AI has also become much more aggressive since the last game, and can defeat you in literally seconds if you're not quick with the fingers. Beating him gives you Model OX, who is — you guessed it, Omega Zero, complete with a crapload of awesome special moves and total badassery.Only not really, since you only get it after beating the game and it's not really that much better then Model ZX.
If you have Zero 3 and Zero 4, you can fight four bosses from each in the same area. Beating all eight gives you the same reward.
And also in Ratchet & Clank: Going Commando, there's a secret boss in Oozla, the Swamp Monster II. It's harder than most other bosses in the game and also rewards you with the Box Breaker after killing it. You can also only get there if you have the Gravity Boots, which you get much later on in the game. You will also probably need the game's most powerful weapons to defeat it.
Dynamite Headdy has a Bonus Boss called "The Money" that is unlockable with a password you get by beating the bonus game four times.
Also, there's a boss in Extra Mode that doesn't appear in the regular mode. Remember that robot from the trailer for the Gamecube Kirby game that became this game? It's the HR-D3, the robot from the end of Kirby's Dream Course that was upgraded with abilities the HR-H from Kirby 64 used. The Metal General EX found it, changed the logo on the front, and used it as a backup in case he was defeated in battle.
Mario Gives Up: Returning to "Area of Bonuses" after pressing all four switches allows you to reach the Key Boss.
Sonic the Hedgehog 2 contains one only found in an updated re-release on iPhone/Android. It's still Robotnik/Eggman, this time dropping spiked balls which need to be under him when they fire back up in order to get him into range. To find it, you need to fall down a bottomless pit in Mystic Cave, a pit which in every other version of the game is a very deep spike pit.
In Professor Layton and the Unwound Future, if you go to the Secret Content and submit a code saved from the second game, you get to do a bonus puzzle designed around the MacGuffin of the second game, and apparently designed by the second game's villain. It's an incredibly hard puzzle, and the villain refuses to let you use Hint Coins, as he wants you to beat this puzzle in its purest form.
All three games in the DS series have a series of puzzles that are unlocked by way of completing the various side quests (for example, completing the mechanical dog in the first game or all the toy car courses in the third). Completing all those puzzles unlocks a final set of puzzles that are the most difficult in the game.
The Archivist in DROD RPG: Tendry's Tale. You get a special ending for beating him, which was meant to require saving up the Hand Bomb to use on him. The developers didn't actually know whether or not it was possible to get stats high enough to defeat him by normal combat. (It is.)
In any version of Initial D Arcade Stage, defeating every opponent in Legend Of The Streets mode will take you to a free battle with Bunta Fujiwara. He is extremely difficult to beat, often sporting Rubber Band A.I.. Whether or not you defeat him, the credits will roll afterwards.
The Smokey Progg in Pikmin is one of these, as you have to go out of your way to find it and it drops an object that produces 100 Pikmin when it dies. It has the difficulty to match as well: just touching its slime trail can kill several Pikmin at once, and any Pikmin attacking the Progg will probably be thrown right into it.
Dawn of War II has two optional missions. One, against the Eldar, has you fight an Avatar of their war god, which is considered to the hardest mission the the game, not just because the avatar is really strong, but because the damn thing calls in lots of vehicles for help. The other has you fight an Ork Warboss, who, while weaker then the Avatar, is still considered tougher than the final boss, though part of that is clearing either of the levels gives you a nice set of Terminator armor and because in the final level, you get to use your entire squad, unlike the rest of the game.
In the Specialist set, getting 70% accuracy or lower nets you Fermion SP, a chart riddled with Fake Difficulty due to sensor bugs when dealing with repeat (purple) notes. What's also agonizing about this is that if you're good enough to even unlock the set (via Special Set 6, where you need to pass the dreaded Son of Sun SP), you'll probably have to intentionally Do Well, But Not Perfect to unlock Fermion SP, so getting there in the first place will leave your HP at a very, very bad value.
In the Conqueror set, there will be a small chance that, instead of the usual boss charts, you'll get Thor TP; given that getting this song is excruciatingly random (or perhaps just insanely difficult, considering the theory that you'll have to get EXACTLY 98% or 94% accuracy), one does not have many chances to practice this song and will have to rely on YouTube videos. A hacked mission in Platinum Crew (in celebration of the Mid-Autumn Festival) spat up a chance to practice it constantly◊ until it was removed, presumably after Pentavision's warning to the Chinese PlatCrew management.
In Technika 2, the Super Speed set brings us D2, a song running at 356 BPM (approximately 1.5 times faster than Son of Sun)... not to mention that to unlock this song, you'll have to play a very, very buggy song called BEE-U-TIFUL, whose difficulty comes from a painfully brutal segment featuring pinks that follow the melody and syncopated repeaters. This song is very likely to leave you in a worse state than if you had tried to unlock Fermion SP in Technika 1.
This applies to all Club Mixing sets in general from the second game onwards, really, with the change in mechanics and criteria on how to reach a boss in a set. Whereas in the first game the boss is determined by the number of MAXes you've accrued during the set, now the boss you play depends on the difficulty of the set you've chosen.
Notable examples from Technika 3:
The high boss of the Sound Lab set is a 2011 rendition of Supersonic by the Pentavision Sound Team. Break! MX is a mandatory song to reach Supersonic. As of writing, Sound Lab is the only way that Supersonic 2011 can be played, outside of the Summer Special Mission last year.
Hyper Speed's high boss is Bamboo on Bamboo MX. The mandatory songs to reach BOB are Now a NEW Day MX and Right Back MX. While not as fast as the other songs in the set, NAND is still troublesome due to the hold note management present throughout. Right Back has one of the messiest new MX charts, as most of the notes tend to overlap with one another. Add to the fact that the screen must register your finger being lifted off, and you'll find yourself accruing Breaks and Misses back and forth.
Fatality, one of the most difficult disc sets along with T2's Maximum set, features a high boss in the form of Xeus MX, which is Thor on steroids, thus in the same league as D2 and Cypher Gate in difficulty. Like other Maniac performance sets, the prerequisite involves playing two specific songs. In this case, they are AD 2222 and Angel. Like other similar charts, Angel's MX chart is designed to push players beyond human capabilities, with (glitch-laden) tiring repeaters being its primary challenge. Many consider this to be HARDER than Fatality's Low Boss (Supernova).
beatmania IIDX is known for having elaborate Extra Stage systems where, on your Extra Stage, you enter a special screen where you select one of several different boss songs. Completing all of these songs and fulfilling certain requirements on them (often a grade and special gauge requirement) will allow you to unlock and immediately play the system's Final Boss.
beatmania IIDX 20 tricoro introduces the "LIMIT BURST" system, which uses crossovers from other Bemani games as bosses.
ADOM has quite a lot of these. Most of them reside in a Brutal Bonus Level and carry some artifact (indestructible powerful unique item) that drops when killed.
There's Rehetep, an undead mummy lord, who "lives" in a pyramid filled with traps and maze-like corridors. The pyramid is impossible to enter until the player character hits level 13, when an invitation from Rehetep will magically appear. The reward for killing him is the Ancient Mummy Wrapping, which grants several very useful resistances and passive abilities.
There's the Minotaur Emperor in the minotaur maze under a ruined city. He carries an axe that deals massive damage, but is also massively heavy.
Dungeons of Dredmor: The real Final Boss is Lord Dredmor himself, but a mistyped code in the third expansion brings you the chance of meeting Vlad Digula, prince of Diggle Hell. He's just about similar in magic prowess to Dredmor, has a bigger lifebar, but what truly makes him nastier is that trying to melee him without massive evasion rates is basically the quickest possible suicide you can find in a game with plenty of them.
Role Playing Games
Chrono Trigger DS had an Alternate Final Boss, the Dream Devourer, which has ties to the final boss of Chrono Cross, the Time Devourer. It is unlocked after you clear all three of the Bonus Dungeons that appear after you defeat the normal Final Boss.
Before that, there's the Dimensional Vortex fights against the Alabaster Shade, Crimson Shade, Steel Shade, and Once-King Dalton.
The Lost Sanctum also has some, like the multiple fights with the Nu Guardian.
The ultimate form of Spekkio is also one of the strongest bosses in the game. But since you need maxed out characters to even challenge him there is not much strategy involved anymore...
The Gargoyle in Koudelka, on Disc 3/4. At the same time, it's also That One Boss - because even for a bonus boss, it is just insane. Also, it's a Hopeless Boss Fight on Disc 2 - when the titular heroine fights it alone, she'll deal no damage and will be forced to run away.
However, the Rewards some of them leave make the rest of the game piss easy. Captain's Hat + Berzerker Mail anyone?
The original game had a few as well. You don't have to fight any of the giant monsters (Obispo, the Roc, the Giant Looper, and Alania). There's also Elcian, a super Looper who appears in the Dark Rift near the end of the game, who puts up a tough fight but gives good experience and loot and can be fought multiple times, making him great for Level Grinding. And finally, 100% Completion unlocks one final battle against Air Pirate Vigoro.
Ragu o Ragula in all of the Wild Arms games for PlayStation, PS2, and PSP. Angolmois also appears in some of them. In fact, the Wild ARMs games have many bonus bosses, often found sealed in crystals found throughout the game. Ragu o Ragula is neatly incorporated into all of these titles as the sleeping demon who is fated to destroy Filgaia, centuries after the conflict-of-the-day is finished off. Big extra credit for overachieving heroes. The other bonus bosses can range from Call Back characters, characters who are no longer a part of the main plot and have been more-or-less forgotten by the main cast, and nudie mags
The Monster Arena monsters in Final Fantasy X, and the Dark Aeons and Penance in the International version. Some of the Dark Aeons were required encounters if you want to backtrack to certain areas. Penance is entirely optional, and he's accordingly brutal... 12 million HP, potent attacks that devastate an unprepared party, and supporting limbs that do even more fun damage.
The Via Infinito monsters, led by Paragon and Trema, in Final Fantasy X-2. Black Elementals with the ability to just use Ultima at 255 magic whenever it wants, Chac for bypassing stone status resistances or debuffing all stats by TEN with Heaven's Cataract or Concherer who isn't too bad but IS a brick wall of defense.
The Fiend Arena in the Internation/HD Rerelease has quite some nasty customers in their tournaments. Expect daunting foes Such as Bahamut with over 100,000 HP and a surehit kill attack for 9999 damage per girl (all used at leisure), enhanced human enemies (Baralai, Nooj, Gippal, etc) with jacked up stats and brand new cheapo moves to annihilate before a chance is had. The toughest though is Allmighty Shinra with potent spells meant to decimate the party right off the bat, and regular nasties such as Paragon and Trema above as regular battles.
X-2 also gives us Major Numerus, a four headed, four staged boss with tons of abilities to decimate the characters. It's required to fight him with Three Iron Dukes equipped (one girl a piece) or else you're just wasting your time.
Hell Wyrm, Yiazmat, Behemoth King, the eight non-story line Espers (which includes Zodiark), Omega Mk. XII, etc. in Final Fantasy XII. To date, Yiazmat is the boss with the most HP in all of Final Fantasy (a grand total of 50 million), and can take multiple rounds to defeat.
The remake in Dawn of Souls for the GBA included optional dungeons with bosses from III, IV, V, and VI, although only Omega and Shinryu from V were much harder than the regular Final Boss.
The PSP remake ups the ante with Chronodia, who has 8 FORMS! It's not a Sequential Boss, though; which one you fight depends on how you did in the Bonus Dungeon prior to fighting her. Either way, she's pretty hard.
Final Fantasy IV had four optional boss fights against Phantom Beasts: Ashura, Leviathan, Odin, and Bahamut. Only one of these was particularly difficult. The others required very specific strategies rather than a highly leveled party to defeat, making them closer to Puzzle Bosses than anything else. This was fitting, as the battles were intended to be tests of your skill. Furthermore, several powerful weapons and armor in the final dungeon are guarded by horribly powerful Palette Swap bosses, including one that hits the entire party with unblockable Doom when the fight starts (giving you a time limit before Total Party Kill).
The GBA version added some more, most notably, a modified version of Easytype Zeromus.
The DS remake removed most of those added by the GBA version, but features two new optional bosses only accessible through New Game+ - Geryon and Proto-Babil.
Final Fantasy VI Advance adds the bonus boss Kaiser Dragon, a monster that was Dummied Out of the original game and, due to having an associated monologue, seems to have been intended to have been a bonus boss in the original version, but to have been cut for time.
In addition to Kaiser Dragon, the entire Bonus Dungeon leading up to him is full of bonus bosses, in the form of souped-up versions of the Eight Dragons, each much stronger than other bosses in the game.
There are also three new boss espers - Leviathan, Gigantuar, and Gilgamesh.
Also, there are five bosses found wandering in a pit within the Dragon's Den - Dark Behemoth, Abyss Worm, Gargantua, Earth Eater, and the Malboro Menaces. All but the Malboros are relatively easy to take down, though. On the other hand, you have the three bosses-in-chests: Neslug, Plague, and the Flan Princesses, which use massive recovery, Doom to all, and Berserk to all, respectively.
Final Fantasy V Advance was especially brutal with these, creating an entire Bonus Dungeon full of them. This included such prestigious opponents as Enuo, the frickin' original creator of The Void, which was the MacGuffin that was Exdeath's entire goal, and something that he couldn't control in the end; Omega MK II and Neo Shinryu, souped-up versions of the bonus bosses of the original game, both of whom made their originals look like marshmallow peeps in comparison (Omega MK. II was very notable, housing a huge floor full of copies of Omega, each one as strong as the bonus boss of the same name, proving just how much stronger the players had to be to stand a chance.)
Keep in mind that all of this being harder than the rest of the game is no mean feat - this was, after all, the Final Fantasy that was denied release outside of Japan first time around due to being too hard.
Ozma (unique in that his difficulty has little to do with inflated stats and almost everything to do with proper strategizing, albeit with more than a hint of Guide Dang It) and Hades in Final Fantasy IX. Kinda complementary - Hades turns out to be a legendary synthesist, and one of the rewards for beating Ozma is something you can synth off to obtain Ark, the ridiculously over-the-top summon.
There's also the Tantarian, another boss whose difficulty is based on strategy rather than just stats. Beating him nets an accessory that teaches the very useful Auto-Haste ability.
Vercingetorix, boss of the final Mission. This bad boy has 15.8 million hitpoints and can't even be accessed until after you beat the game. But it's easier to beat by simply poisoning him and then guarding for the entire battle; this is because poison deals damage based on maximum HP, and Vercingetorix, as mentioned, has a lot of it. Long Guis, however, are immune to every form of status debuffs.
Long Guis also qualifies, having even more HP and huge stats.
Final Fantasy XIII-2 features several optional bosses, three of which are absolutely brutal. The Long Gui returns, and despite only having a quarter of the HP it had in XIII, it's still extremely tough to put down. Yomi is a weaker (but still formidable) version of Vercingetorix. And finally, there's Raspatil, a horrifyingly powerful Undying Cie'th that's probably the hardest fight in the vanilla game.
The DLC Coliseum battles are all nasty, especially Jihl, the one person everyone who played XIII wanted to kill and now can't because of her summoning tricks and Sadistic Surge, and Gilgamesh, who has almost 10 million HP, can heal himself for 1 million after stagger, and once he reaches half HP, he goes into enhance power mode, complete with auto-haste and attacks that even a Sentinel can struggle to keep up with.
The most notorious monsters in the Coliseum, however, are Snow and Valfodr. First off, before you can fight Valfodr, you fight Snow, who has 10 million HP, and if you don't provoke him into attacking someone else and he continues to attack the same character for a set amount of time, he will use a Total Party Kill attack that you cannot survive even if you use Sentinels.
Once you defeat him, you fight Valfodr. He has five forms, progressively getting harder. While Level 1 and Level 15 aren't too much to be concerned about, at Level 45, he summons monsters that constantly heal him and gains a powerful axe attack. At Level 70, he summons Chichu - the ever famous best commando in the game - and gains a group attack that can kill even a triple Sentinel party (Reprieve won't save you either). And while he doesn't summon anything at level 99, his attacks are even more powerful, and he's much quicker.
First game: The Clock Tower Phantom (gives you the last Stop spell upgrade), as well as many of the tournaments.
The international release addedSephiroth (bragging rights), Ice Titan (bragging rights), Kurt Zisa (bragging rights).
The Final Mix version adds in the international bosses, gives you decent rewards for beating them (extra Keyblades for Seph and Ice Titan, and the Zantetsuken attack for Kurt), and adds the Unknown, who is later revealed to be Xemnas, the Big Bad of Kingdom Hearts II.
358/2 Days: Dustflier. He can be found before beating the game, in a late-game mission where the goal is to defeat six bosses scattered through Twilight Town in succession, and only appears after all six are dead. And while you can complete the mission by only taking out the first six, you have to go and finish Dustflier to fill up the extra portion of the Mission Gauge, which is part of 100% Completion. (Fortunately, 358/2 allows you to redo missions at will.)
Birth by Sleep brings its own Bonus Boss, Vanitas Remnant, notable in that he only has one health bar because he's JUST THAT HARD TO HIT. If you heal yourself during the battle, he also heals himself. Completely. Unless you use potions instead of magic. The Iron Imprisoners are a much less difficult example.
Birth By Sleep's international release adds a new boss, the imaginatively-named 'Mysterious Figure,' revealed to be a time-traveling young Xehanort in Kingdom Hearts 3D, a black-coated, dual-laser-blade-wielding mofo clearly in the same style as the first Final Mix's just as imaginatively-named Unknown. This boss has put the rest of the series's famously batshit hard bosses to shame. So far, the only known strategies for beating it are "Spam Dodge Roll with Ventus and pray" and "Spam Thunder Surge with anyone and pray".
The Final Mix adds three more that can be fought in the Mirage Arena: Monstro and the armors of Master Eraqus ("Armor of the Master") and Master Xehanort ("No Heart").
Dream Drop Distance has Julius, featuring heavy defense and powerfully strong attacks. Not to mention one of his combos doesn't set off Once More, only Second Chance, meaning you WILL die if you're unlucky, and another attack so powerful that not only does it eat up basically all of your HP, but it disables your active command. God help you if you only pack one curaga and kept the cursor on it. The worst part, the only way to know which way to dodge for the attack is to use the bottom screen, which you never use during any other fight, to see where his icon is headed. And you're not allowed to bring your Dream Eaters into the fight.
Pokemon Redand Blue: Articuno in the Seafoam Islands. Zapdos in the Power Plant. Moltres on Victory Road. Mewtwo in Cerulean Cave after you become Champion. The use of cheats also enables the player to battle Professor Oak in the original Red/Blue versions, with a team of higher levels than the freaking Champion. Some fans speculate that he was a supposed to be a True Final Boss and got removed from the storyline, but the producers forgot to remove his battle data, since Boss Rush Agatha of Elite Four states that he is a Retired Badass. Sadly, he didn't get any battle data in FireRed/LeafGreen.
Pokemon Gold Silver And Crystal: In the first Generation II games, the legendary that's not your version mascot also counts as a Bonus Boss; in Crystal, both Ho-oh and Lugia also count, with Lugia being available only by talking to a man in Pewter City and Ho-oh only being available by catching the Legendary Beasts. Red in the second generation (though it's debatable whether he's this or the True Final Boss, since the credits roll after you win). HeartGoldandSoulSilver have a boss Trainer that can only be fought by having a Celebi: Giovanni. This Trainer isn't very difficult, however, and mainly serves to tie up some loose story ends. Those two games also have a bonus battle with Red, the player character from Pokémon Red and Blue. He is the toughest trainer in the games to date, with all of his Pokemon over level 80. You have to massively level grind after the main game or transfer Pokemon from other games to stand a chance against him.
Pokemon Ruby Sapphire And Emerald: Latios/Latias and Rayquaza in Pokémon Ruby and Sapphire. In Emerald, Rayquaza can be captured before you take on the Elite Four in Emerald (and Groudon and Kyogre take its place as Bonus Bosses). Steven turns from Final Boss in Ruby/Sapphire to Bonus Boss in Emerald, having stepped down from his position as Champion. You find him in a secluded cave in Meteor Falls with a team identical to the one he has in Ruby/Sapphire, except twenty levels higher. The 7 Frontier Brains at the Battle Frontier also count, as they are only available after you beat the Champion.
Pokémon Black 2 and White 2 basically goes Up to Eleven on this one, letting you battle nearly all of the previous Gym Leaders from Generations I-V, from Brock to Drayden, in the Pokemon World Tournament or PWT. If you manage to conquer the regional tourneys and the World Leaders tournament, you get to fight all of the previous Champions (minus Iris) in the Champions League. Also, there is also Colress, the Shadow Triad, the Striaton Trio (Cilan, Chili, Cress) in a Multi Battle, now Retired Badass Alder, his grandson Benga, the GameFREAK trainers, and under the right conditions, Cheren, Bianca, and N. There are plenty of powerful trainers to battle for the postgame.
Pokémon X and Y doesn't have as many of these bosses as the previous generation did. For Legendary Pokemon, there's one of Kanto's Legendary Birds (Which one you'll face depends on the starter you picked), Zygarde, and the aforementioned Mewtwo. As for trainers, it is possible to challenge Calem/Serena to a rematch postgame, and going through Looker's postgame missions has you battle Essentia four times in a row.
Aec'Letec in the Expansion Pack of Baldur's Gate. Although he's more of a Final Boss to the expansion pack, said expansion pack is an optional sidetrack from the main story, he can be safely skipped after finishing Durlag's Tower and is much worse than the game's actual final boss.
Kangaxx in Baldur's Gate 2, who could only be hit by +4 weapons, and, in his demilich form, could cast the annoying insta-kill spell Imprisonment at will, which had the tendency to mess up romances if your love interest got hit. Kangaxx does have an Achilles' Heel, however, in the form of a shockingly poordeath save for his level.
Most of the dragons in the game are also optional fights, though they give some good rewards after being slain.
There's also an optional (and completely story-irrelevant) fight against some demon knights in the Underdark.
In the expansion pack Throne of Bhaal, the Bonus Boss was Demogorgon, an incredibly powerful demon imprisoned at the bottom of Watcher's Keep.
The Twisted Rune is an order of evil spellcasters who, when you enter their lair, assume that you've come to foil their plans and attack you. They're sensibly skeptical if you claim to have found them by accident, because the only way that would happen is if you were wandering around a bad part of town while carrying an incredibly rare and valuable type of gemstone and opening doors at random. (This is in likely exactly what happened, unless you looked at a guide. The clues that would lead you to them were never put into the game.)
Divine Dragon/Divinegon in Dragon Quest III became available to fight after beating the game. You even needed to beat him five times to gain access to all of his wishes.
The Game Boy Color version of this game introduced yet another bonus boss, GranDragn. Getting to this boss required you to complete such a long, boring, and ridiculous fetch quest that even the most hardcore and dedicated gamers have never seen him.
Dragon Quest VI has Nokturnus (better known as Dark Dream), who, thanks to his appearances in the Monsters series, is considered by many to be the quintessential Bonus Boss of the series.
Nokturnus actually gets a little more plot relevance than the average Bonus Boss, in that during the story, you witness a king try to summon him to deal with the Big Bad, only to be violently reminded that Evil Is Not a Toy. Though, if you're strong enough to put Nokturnus in his place, he really will deal with the Big Bad on your behalf.
God in Dragon Quest VII. And the four spirits, which is the odd thing since they are supposed to be weaker storyline wise than both the Last Boss and God, yet you can't fight them unless you can beat God easily.
The Dragon King in Dragon Quest VIII. Have fun with the Darksteel Dragon as well; he's basically a Metal Slime with a lot better attack, who attacks three times, and, just for more fun, he has nearly 2000 HP.
Half of the bosses in Dragon Quest IX. Of special note are the grotto bosses, who are revealed to be fragments of the Grand Architect Zenus, and the legacy bosses, the final bosses and some midbosses from every previous serial title (e.g. Dragonlord, Zoma, Estark, Rhapthorne, etc.) The best kind of Pandering to the Base. You can even opt to give the legacy bosses the experience you gain from beating them, and they will level up each time, to a max of 99.
In the SaGa series, most of the game is optional, including many of the bosses. SaGa Frontier does have a few optional bosses who are particularly difficult, including the Earth Dragon in the Bio Research Lab, and cheating bastard Jotnar, who likes to employ his most powerful attack four consecutive times on his second turn.
Golden Sun had Deadbeard, an undead pirate found at the bottom of Crossbone Isle, who guards the game's most powerful armor. One path to him contained another bonus boss, a weather controlling lizard. A third bonus boss had its own bonus Town outside the Bonus Dungeon, and was a gigantic acid frog.
The Lost Age gave us the Star Magician, Sentinel, Valukar, and Dullahan. The Star Magician summons mooks to use Jupiter psynergy on you, buff and heal the Magician, and explode for huge damage. Sentinel constantly buffs his defense and is immune to all psynergy, meaning he gets tougher and tougher. Valukar can knock your Djinn into Standby and use your summons against you with Crucible. And Dullahan can put every active party member's Djinn into recovery with Djinn Storm, gets three moves per turn, and hits like a runaway cement mixer.
In Dark Dawn, Star Magician and Dullahan get buffed up, with Star Magician getting three new mook types (Curse, Death, and Ghoul) and Dullahan getting Valukar's Crucible move. There's also the Ogre Titans, a group of five increasingly powerful physical attackers, and the Ancient Demon, who can take over one character with Demon Sign.
In the early parts of Dark Dawn, if you try to beat the Psynergy Training Grounds a second time, the Dim Dragon gets an upgrade, making it an early-game Bonus Boss.
Tiny martial arts master Jinx, who you must fight three times (after defeating his apprentice, Jagger). The boss lives in Monstro Town.
Final FantasyShout-Out Culex, a powerful magic-using entity from another dimension who attacks using four elemental crystals and is quite possibly harder than the game's Final Boss. It too lives in Monstro Town.
There's also Mokura, a green cloud monster that appears randomly in Belome Temple and has boss music playing during his fight, although he's not nearly as tough as the other two.
Bloopers who shows up every time you find a new shortcut in the sewer. Kent C. Koopa also blocks a road and makes you pay to pass; beating him lets you pass for free. Then there is a Dojo, where you can fight for bragging rights. The final blooper, Kent C., and the Dojo Master could all give Bowser a run for his money if he didn't have the Star Rod.
There's also the Anti Guy, found guarding a chest in a dungeon halfway through the game and with HP and attack roughly on par with Bowser's penultimate form. He can be beaten straight-up, or you can exploit his Sweet Tooth to bribe your way to the chest's contents.
In Chapter 8, if you intentionally flunk a quiz from one of the Bowser-faced stone doors, your punishment will be a No-Holds-Barred Beatdown against three Anti Guys. Easily the most difficult fight in the game, as Mario will initially be taking in the ballpark of 25-30 damage a turn with (unlike all the above bosses) no way to cheese your way out of it.
Bonetail gives the game's final boss a run for its money (which is lampshaded by Goombella) and requires going through a dungeon with 90 consecutive battles (99 floors with a "breather" every 10) to reach him. He is a bit easier than the final boss, as you'll probably be better equipped and levelled by the time you reach him, and his attacks aren't as complex to deal with - he just has enormous attack power and endurance, and getting to him is a massive two hour-long ordeal.
Atomic Boo, fought in Creepy Steeple if you enter the main hall and take the Spin Hammer attack to the swarms of Boos enough times. He isn't particularly hard, but knowing he even exists is a bit of a Guide Dang It.
Super Paper Mario tripled it, though (unless you count Francis in chapter 8-2 as one). The first of the three bonus bosses was really another version of the game's first boss. To even face the second boss, you have to clear a dungeon filled with even stronger enemies that are all pitch black, making distinguishing subtypes near impossible without Tippi/Tipptron until it's too late.Twice. The third is the 100th Sammer Guy, End Boss, who, although weaker that the second Bonus Boss, is the only one that cannot be fought until after beating the final boss.
During your first encounter with the Sword Dancer, you may or may not get fucked up almost immediately. His attacks are absurdly powerful in this encounter, being able to KO the ENTIRE PARTY with a single attack. Though, if Raine unlocked one of her spells, like the photon spell, then you can defeat it rather easily. The next two encounters are only moderately hard because you'll be appropriately-leveled and you'll be able to use Unison Attacks.
You fight Garr, Farah, and Meredy in the coliseum. They are absurdly hard to beat, in fact, think of having to fight Lloyd, Genis, Zelos, and Presea at the same time, while they use the very same battle strategy as you do, which is what makes them so hard. But once you get rid of Farah, then Meredy and Garr are almost a piece of cake, that is assuming you have enough healing items. The best party to fight them with are Lloyd, Zelos/Kratos, and Genis. Replacing Genis with Raine is also a good idea, but her lack of offensive spells may cause the fight to drag on. It's kinda funny hearing Lloyd say "Who the hell were those guys?" after beating them.
Tales of Eternia had Sekundes, the summon of Time, although you didn't have to beat him to enlist his services. Maxwell and Shadow were also technically optional, but you did have to beat them. Cless gives you his bandanna and the Eternal Sword if you beat him in the Arena, and Valkyrie stands before a lot of treasure chests. Things like this make Eternia end up a very long and interesting game.
The "Traitor to the Heavens" (Kratos fulfilling the role of a cameo boss). It also has a bit of an odd case with the Radiant Winged One, who, while entirely optional, if the player opts to fight him, ends up as the last boss anyway.
The PS3Updated Re-release adds several more optional bosses, such as Clint of the Hunting Blades, the Sword Dancers which reward you with Flynn's normal, non-Fell Arm Infinity+1 Sword, and the Spiral Draco, lord of the Entelexeia and possibly the most difficult boss in the entire Tales Series.
There's also a colosseum fight where you use the four characters you currently have in your party against computer controlled versions of the other four you aren't using.
In addition to the already long list of bonus bosses in Vesperia, there's also Yeager's bodyguards, Gauche and Droite.
Tales of the Abyss contains Nebilim, who's practically impossible to beat on your first playthrough, as well as Reid, Mint, Nanaly, and Philia.
The post-game boss Solomos, as well as all the other bosses in the Zone Cage and Coliseum (including Veigue, Kohak/Amber, and Reala as the previous Tales cameo battle and Poisson. Defeating Solomos also changes the real final boss, Lambda Angelus into Lambda Theos. In addition, you can re-fight your first boss, although he is no longer the Warm-Up Boss that he was before. You also can fight the incredibly large and strong Rockgagan, although in the PS3 version, you only really get a trophy for defeating him - not even experience points.
There's also the three dragons that correspond to the 3 Giant Cryas in each country. Good luck trying to take them on before beating the final boss cause even on Normal, it's not easy.
Tales of Xillia has the Golden Swordsman at the end of its Bonus Dungeon. He's nothing to scoff at the first time you fight him, but he gets even stronger the next few times you fight him.
Tales of Xillia 2 has a massive number of these compared to its prequel, all available after beating the game. Defeating all of the Giganto Monsters will result in all of them reappearing as their much stronger EX versions. The bonus dungeon is populated by shadow versions of numerous past bosses, your party members, and Stahn and Cless. The end of EX Tag Arena pits you against powerful versions of past bosses partnered with random members of your party, plus if you defeat them quickly, you'll be rewarded with a bonus fight based on who your lead character is (Most notably, in Ludger's case, a stronger version of the final boss shows up). Lastly, the end of EX Team Arena pits you against the cameo team of Cless, Mint, Stahn, and Rutee in a battle that's chaotic enough to warrant a special ending scene should you prevail.
Also, Tales of Hearts bonus boss is nearly IMPOSSIBLE without use of infinite aerial combos or cheats.
The four-legged Dragons (not to be mistaken with the two-legged wyverns) in Monster Hunter, as well as Kirin the lightning unicorn.
Dark Souls has several in the optional areas of the game. The first one most players see is the Stray Demon, a much stronger version of the tutorial's Asylum Demon that drops a highly valuable Titanite Slab. Others include the magical Moonlight Butterfly in Darkroot Garden, the illusionist Dark Sun Gwyndolin in his father's tomb, and the half-Dragon Priscilla in the Painted World. The difficulty of these encounters depends on the player's progress through the game and they are much easier than the final boss, but they still provide a unique challenge to those who look for them.
The Downloadable ContentArtorias of the Abyss adds a new hidden Bonus Level with several bosses in it, all of them difficult fights. The bonus content even has its own bonus boss; while most of the bosses block off new bonfires and are normally accessible, the black dragon Kalameet is unlocked by a side quest and only gives the Calamity Ring as a reward, which halves your character's health. Cutting off his tail creates a powerful weapon, but doing that is even harder than killing him. Adventurous players can also find a fight against two of the first DLC bonus boss at the same time.
The Ancient Dragon is a brutal Marathon Boss with a lot of health and all of its attacks can kill you in one hit unless you have extremely high Fire resistance. The saving grace is that most of its attacks are fairly telegraphed and can thus be avoided rather easily. Except when it decides to fly up and rain fire on the arena. Avoiding that can be a struggle. Upon defeat, it drops an item that makes the next Bonus Boss easier.
King Vendrick is an Anticlimax Boss whose attacks are slow and easy to dodge, though he can kill you in one hit if you aren't careful. However, he is also a Puzzle Boss since his defense is incredibly high, making him impossible to defeat if you don't have Giant Souls in your inventory. Upon defeat he drops nothing. The rewards appear behind a hidden locked door in a different area.
The Darklurker is the most obscure. The previous two are at least encountered in the storyline. It is entirely possible to never encounter this boss if you aren't playing with a guide. You need to discover and join an hidden covenant and fight through three small dungeons filled with dangerous black phantoms just to meet the Darklurker. Your efforts are "rewarded" with a harrowing battle against an eerie angelic figure who hurls powerful pyromancies, hexes, and sorceries at you while flying around the arena. It thankfully has much lower health than the other two bonus bosses. Upon defeat, it drops its soul which can be traded for a powerful hex. Its defeat also maxes out devotion to the hidden covenant, which comes with its own rewards.
In the Mega Man Battle Network series, there is so much extra content and so many bonus bosses that the time taken to defeat them is longer than the main story line. In all of them, however, you face Bass/Forte. Unlike other continuities, here he is a god-like Badass.
The sequel series, Mega Man Star Force is similar, although it doesn't take nearly as long to do so. Usually there's a secret area after beating the Final Boss where you have to fight upgraded forms of each boss in the game, followed by an all-new secret boss. After doing that, the storyline's final boss is upgraded, with it being the truly strongest boss in the game. The only exception to this is the second game, where after beating the upgraded final boss, you fight an upgraded Rogue after the credits finish.
You can also engage a number of repeatable bonus bosses and random people who can Wave Change in 2. These include second shots at the storyline bosses to get their Mega cards, plus farmable bosses like Kung Foo Kyd, Gemini Spark, and Cancer Bubble.
In addition to the aforementioned styles, the third game has a rather unusual take on this with the Omega versions of the bosses, as they can rarely appear virtually anywhere in the game, and also at any point in the story, even before you've fought their regular versions. It's entirely possible to run into one of them right after the gameplay tutorial, despite even weakest of them being far stronger then the final boss. Fortunately, the game is nice enough to not give you a game over for losing to them and also alerts you of their presence by changing the music in the area to a very ominous tune.
Mega Man X: Command Mission, meanwhile, had two Bonus Bosses plus another set of nine. Rafflesian and Duckbill Mole gave X, Zero, and Axl new abilities that were useful in what remained of the game by that point. Ninetails and the preceding eight Tails Clan members, on the other hand, who were definitively even more this trope, could only be fought after beating the final boss, making the rewards for beating thempretty much awesomely worthless.
The 3 Golden Pigs at the end of the Bonus Dungeon (Mull's Dungeon) in Atelier Iris, which are significantly more difficult than the final boss.
In Atelier Iris 2, the fights at the Dragon's Nest, particularly the last one against 3 Instant Brownies. However, while they are more powerful than the last boss, the overly-easy battle system makes them no more difficult than anything else, provided the player has stocked up on resurrection items.
Kisuke in Bleach: Soul Carnival 2. The thing with him, though, is that he can be fought pretty early on in the game, not that you'd have any chance of survival then. Until you clear the Soul Society missions, he'll probably kill you with just one combo. Not to mention that he has two supports, whereas most bosses only have one, OR the fact that his Burning Attack can even hit you if you're off-screen, and it stuns you invariably (as Burning Attacks never miss). When you defeat him, you'll unlock him as a playable character.
Breath of Fire III had the Berserker, difficult because it attacked for three to four hundred damage, and often attacked several times before any of your characters got to. Worse, it was a random encounter on the way to getting one of your dragon genes, and was a normal monster.
And in the same area was an even tougher Bonus Boss, the Arch Mage. He has far less HP than Berserker (only about 3,000 compared to the Berserker's 15,000), but regenerates 1,500 of it every single round, which is more than most casual players can deal in a single round, and is capable of hitting just has hard as Berserker. In fact, if you have one living and two dead characters, Arch Mage will USE A SKILL THAT REVIVES THE TWO CHARACTERS. Presumably, he does this simply as a means of embarrassing you further.
Breath of Fire IV has Rider as a hellish random encounter in Mukto. With 40,000 HP he is already a tough opponent but he also regenerates 20,000 HP every turn...try to overcome that.
Breath of Fire: Dragon Quarter had Dover, who was the final boss in the Bonus Dungeon. As long as you have a high enough level (around 50), he's not that bad. The only problem is is that his defense switches from regular ol' attacks to Dragon defense. So your time limit is based on how much you have left on the D-Counter. Lin's/Rin's "Shatter!" technique is particularly effective here.
The Demi-Fiend battle in Shin Megami Tensei game Digital Devil Saga, quite possibly one of the hardest bosses in the history of JRPGs, if not the hardest boss. Not only will he instantly kill you in the first turn if you have a "forbidden" move set (read: any passive or castable move intended to null, absorb or repel enemy attacks), but the strategy required to defeat him requires a very specific use of one usually worthless skill that you would never use in the main game (to wit, the Null Sleep skill, which nulls all damage one would receive while asleep). I have no clue how anyone could figure this out without the use of a strategy guide. Beating him unlocks an useful accessory that you can find midgame through the sequel.
And even then, if you do manage to get him down to half health, his High Pixie will fully heal him. If you kill all of his demon companions, he'll insta-kill you. If you go in with any protective moves, he'll insta-kill you. Hell, even with the correct strategy, if you take too long to kill him, he'll just get bored and insta-kill you anyway. To add insult to injury, his battle music is the regular Nocturne battle music, so he may be an uber hard bonus fight to you, but you're nothing more than a random encounter to him.
Satan in the sequel is likewise enormously difficult, if a lot less so than the Demi-Fiend; you require to continuously cast Charge to boost all your stats to max so Satan won't cast God's Breath, his insta-kill move. If you did so, good, he'll only cast Dekaja and put you back at square one. Hurt him enough and take too long and he will cast Diarahan, putting himself back at full health. Anyway, even without their instant kill skills, both are beastly difficult — you need to cap out your major stats to even have a fighting chance, and thenthere's the actual strategy involved... which simply fails half the time due to bad luck.
Other Bonus Bosses in the duology include:
The Four Gods: Each appears in a different sector in the first game, each representing a specific element. Avoid repelling their elemental attacks or hitting them with their respective elements and they will go down fairly easily.
Huang Long: Appears high in the Karma Temple after killing The Four Gods. Hits like a truck with the Almighty-type Celestial Ray, which also slaps you with any ailment he wants. Has tons of HP and can cycle through several forms to make the task of damaging him harder. Still not as hard as the Demi-Fiend.
Beelzebub's two forms: Baal Zabul appears in Svadhisthana's underbelly once you unlock it with the Red Key. While he is somewhat strong, he's really nothing to be worried about. Beelzebub proper appears after Baal Zabul's defeat in the Manipura Waterways, and comes back with a vengeance, packing the lethal Death Flies move, which will kill anything not protected against Dark attacks with 100% effectiveness. Even if your charaters are protected, it will hit with a horribly strong Almighty-type attack.
Orochi is the last obstacle in the path to the Red Ring, required for another boss. He has eight actions on his turn, can exploit elemental affinities and Criticals with Ice and Lightning attacks, abuse Makakaja and Megidolaon, and has a crapload of resistances. However, he has pathetically small MP for a boss, and will try to restore his tanks with yours. With Null Mute, he turns into a joke after a few turns.
Metatron fights you after you enter Ajna with the Red Ring. He likes to abuse Makakaja, Revelation, and Fire of Sinai, which can hit several times for Almighty damage with the possibility of instant death.
King Frost appears at Coordinate 136 after the defeat of Mick the Slug. Finish the minigame of "find the key" and King Frost will appear at the Princess' Bedchamber. He spams Cocytus, which will almost always freeze, and summons overleveled Jack Frosts to pound you.
In the second game, there are fights against the Four Archangels, Shiva, Vishnu, Jack Frost and Seth in the second. The Shiva and Vishnu fights also require you to find a special item for each, from Parvati for Shiva and Narasimha for Vishnu.
Shin Megami Tensei I and Raidou Kuzunoha vs. The Soulless Army has Beelzebub. Soulless is particularly vicious as he requires three items to be fought, all of which have to be acquired through Zerg Rush battles with 100 enemies each; these will tend to be Demonic Spiders. Then, he will be fought amidst anotherZerg Rush. Pray none of your healing demons get Charmed, as he will use and abuse any attacks which can inflict said ailment to jack up his health.
Shin Megami Tensei: Strange Journey has the NGP-exclusive Alilat and Demiurge, as well as Mother Harlot if your alignment is Law at some point after the Dual Boss fight against Aniel and Kazfiel. (Note that you only have to be Law-aligned to unlock the door to her chamber; you can change your alignment afterwards, which allows you to face both Mother Harlot and Bishamonten, whose chamber has a similar lock to the Chaos alignment, in the same playthrough.) Alilat has the game-breaking combo of high Magic stat, Mind Charge, and Megidolaon-a nigh-guaranteed Total Party Kill. Demiurge is a Barrier Change Boss, has the even worse Big Bang, which deals even more raw damage than Megidolaon and Dekunda and Dekaja, regularly heals himself with Diarama, and has a ton of HP. Additionally, he's fast enough to dodge most of you attacks and has all of the deadliest elemental spells. Mother Harlot uses the Almighty skill Babylon Goblet, which is more powerful than Megidolaon and also has a high chance of causing Charm.
Shin Megami Tensei IV has both the Fiends (Matador is one example) and the DLC Bosses (The Four Archangels, Ancient of Days, Sanato, and Masakado.)
The game also has a plethora of bosses that can only be fought in their respective challenge quests. While the majority of them pale in comparison to the monsters already listed (the main exceptions are Beelzebub (of course) and the New Game + exclusive Astaroth), they still count since most challenge quests are optional. Other than the aforementioned opponents, there's one particularly strong Bonus Boss for each route (though they don't compare to the Fiends, DLC Bosses, Beelzebub, and Astaroth, they're still stronger than other Challenge Quest bosses): Mastema for Law, Demiurge for Chaos, and Shiva for Neutral, with the first two coming form Challenge Quests and the last being the Terminal Guardian's final battle.
Special mention must go to the Fiends. Seven of these Fiends (Matador from above being one of them) can only be found in certain locations and the chance of actually encountering them is very low (1 out of 256). Each one has at least five Press Turn icons, will always get the first strike, and will spam Antichthon (massive Almighty damage and all stats lowered) if they cannot safely attack you or your demons with their preferred attacks. Defeating them will unlock them for special fusion, and often, a wonderful reward, including some of the game's best equipment.
Persona 2 was the Persona series' first entry in this list with Philemon's brutal bonus battle on his EX Dungeon.
Persona 3 has Elizabeth, although she can only be fought on the second playthrough by accepting her 55th request and going to the top of Monad. Although she seems to be nothing more than a thin blonde girl dressed like a bellhop, she is the most powerful foe in the game, can only be fought one-on-one (she'll kill any other party members right away), gets to attack twice every turn (where you can only attack once), has multiple personas and powerful attacks, and heals herself completely when at low health. Even worse, if any of her attacks are nullified, reflected, or absorbed (which they invariably will be, considering her attack rate and huge range of attacks), she goes berserk and spams a 9999-damage attack (out of max possible HP of 999) nonstop until you die. Amusingly enough, the Updated Re-release version of the game features an upgraded version of your starter Persona which seems to be tailor-made to fight her, as it resists every type of attack, giving you a good overall defense against anything she tosses out and avoiding driving her berserk.
While nowhere near as insane as Elizabeth, the Reaper that can be fought in both version of P3 is no slouch when it comes to making a normal player tear their hair out. It's fond of casting spells that hit the whole party for 700-800 damage and going insane on unblockable "almighty" spells if the player sets up reflecting items. This one is more infuriating to the average player due to the fact that he appears when the player spends too long in Tartarus, the game's central randomly generated dungeon.
Persona 3 Portable allows you to fight Elizabeth's brother Theodore if you make the proper choice early on in the game (it's not dependent on gender, apparently). However, it cranks things up to 11 with the Vision Quest, which not only contains more difficult versions of the Arcana Shadows, but also allows you to fight Margaret! Yes, the one in the next example. You can still use your full party, but that doesn't make things any easier...
Persona 4 continues the tradition with Margaret. While you can bring in party members and she won't (immediately) wipe them, she's just as frustrating. Nice changes include only healing once. She'll still 9999 Megidolaon you if you bring in a forbidden item, and dump lesser ones on you every 50 turns. She'll also exploit 1 More relentlessly if you give her the chance in the pattern.
Devil Survivor brings in the Fallen Morning Star, Lucifer, for its battle. While insanely difficult (infinite range, level 99, etc.), beating him does give you the ability to fuse him. Most people just take advantage of the fact that Recarm gives the revived the next turn to attack, and just suicide run him.
Though your strategies are moot if he manages to get Megidoladyne off a couple of times, since every cast boosts its power until the 4th/5th is LETHAL. The first already does 500-600 on everyone!
There are a bunch of other, lesser bonus bosses as well.
Ghost Q shows up on Day 3, offering treasure. If you select the correct card (it's totally random), you can complete his stage without having to defeat him, but the other cards turn into doubles of him.
Ikusa shows up with a swarm of powerful undead on Day 5. He revives the ones you defeat, and furthermore, you have to prevent any of them from reaching a pair of escape points while you battle him, then clean up after he's gone.
Also in Day 5, Nebiros. He appears surrounded by a lot of Vile demons with healing capabilities, meaning he can hide behind them and hit you from afar.
Sage of Time shows up on Day 6, hypnotizing civilians. If any of them make it all the way to him, he'll take their souls and you get a game over. You can wake them up to get them to start heading away from him, but if a demon gets them before they get away, same result. Later on the fight, the Sage will brainwash more civilians into entering.
Devil Survivor 2 has a whole slew of these (Ghost Q, Sage of Time, Billiken, Belial, Nebiros, Lilith, Beelzebub), culminating in Alice, each with a different gimmick:
Ghost Q shows up at a time when you only have the MC in the party—you actually can get one other character into your party before engaging him, but he won't fight you. Also, if you defeat all of the other demons on the field before finishing him off, he'll run away.
The Sage of Time will fight you with mid-tier demons when you're far too underleveled to be able to equip any of the heavier-hitting moves in your arsenal.
Belial will hit the entire map with Gomorrah Fire, so you and your demons need to, at least, Null Fire.
Nebiros will appear in a gaggle of undead and continuously summon more if you kill them, and Body Surf into them if you instead choose to go after him.
Lilith sics a bunch of hypnotized civilians which you have to avoid killing with immensely strong demons, and her Temptation skill will wreak havoc amongst enemy leaders. Worse, any male leaders hit by Temptation will be charmed without fail, even with Null Mystic. Female leaders aren't charmed just as unfailingly, but there is a chance Lilith can charm them anyway.
Billiken is a fairly standard battle, except his battle is the first one in which you can crack Holy Dance, and unless you abuse the hell out of the movement skills, he's programmed to go straight for the Pazuzu that has it and one-shot it. He can also steal money from enemies; if he manages to deplete your wallet, he can hit you with Barrage Strike, which hits for a lot of Almighty damage.
Beelzebub is a vicious Barrier Change Boss with a nigh-flawless defense and incredible attack, with a continuous stream of overleveled mooks.
Finally, Alice isn't as difficult as Lucifer, but she does have Belial and Nebiros fighting with her, both with their signature tricks. Alice herself can easily oneshot entire parties with Die For Me!, remotely drain them to death with Vitality Drain, revive Belial and Nebiros, and speed up their turns. Belial doubles as a callback to the first Devil Survivor.
Tholapsyx the red dragon. Quite possibly the hardest boss in the game, thanks to her size and fire attack; buffing the entire party (preferably with Energy Immunity: Fire and Stoneskin) and micromanaging spellbooks is almost mandatory, as opposed to the final bosses, whom you can just whack with sheer force if the party is well-equipped. The reward is 200,000 gold for your keep plus an insane amount of loot, including a cool weapon for paladins and clerics who bothered to take a certain quest in the keep.
Mask of the Betrayer has its own bonus boss, a seemingly harmless badger spirit that turns into a Gigantic Angry Badger of One-hit-kill Doom if you manage to anger it. Killing it nets one one of the only items in the game to grant permanent haste status (barring the time-consuming item crafting).
In Storm of Zehir, you can encounter One of Many on the world map, who will probably be impossible to beat the fist time you encounter it (you're thankfully not forced into a fight with it). However, due to the Wide Open Sandbox nature of the game later on, you can return and fight it once you're sufficiently leveled. Beating it will earn you the Imarskarcana, a helmet with good spell resistance, the ability to summon a demon once per day and a few other perks. If you don't want to fight it, you also have the option to feed it your companions for experience points.
To start off, by the middle of the game, you can meet the first Bonus Boss, Wyvern, who is probably about 30-40 levels harder than your current, probably level 20s characters. Then you'll eventually meet three more bonus bosses, Golem, Alraune and Manticore; the former is a seriously extreme Mighty Glacier, the second loves to spam Standard Status Effects, and the last one combines both.
Most excruciating are the four post-game bonus bosses: The three dragons and Primevil. Each dragon has a breath weapon that can instantly wipe out your party on turn one. You can't beat them without having a protector with antivolt/antifire/anticold lvl.5, and Primevil has all three of those instant death attacks, so your protector has to have all three anti skills, and you need a turn guide so you know when to use which antimove. And you can still outright die if he uses his "disable all skills of all characters" move. You had to pray he didn't use it, or kill him very quickly. Good times, good times.
Its sequel, Heroes of Lagaard, also has a slew of bonus bosses. The dragons return, as well as a new True Final Boss and even more Side Quest bosses, some of them already accessible before you beat the game.
The next sequel, The Drowned City, doubled the number of bonus bosses from the previous games, both new and recurring, and this time, there are far more Bonus Bosses you can unlock via Side Questsbefore you beat the game even once. Cue the much-needed level grinding for the Bonus Dungeon.
Panthera Cantus from The World Ends with You is the toughest boss in the entire game. It has the highest attack power of all the Noise and two separate bodies; a tiger on top and a lion on the bottom. The fight itself can be quite hectic and requires the player to pay absolute attention to what is going on in both screens.
In addition, there are four "Boss Noise" on various days (Progfox, Grindcore Minks, Wooly AOR, and Goth Metal Drake), blue Noise symbols that lead to fights against much stronger Noise than average. For 100% Completion, you have to beat them all on Hard. Feel free to whimper.
And in addition to THAT, additional Boss Noise symbols for every non-Bonus Boss except for the Final Boss appear on various days after beating the game. This is more of a convenience for those going for 100% Completion, since you don't have to go through the entire chapter to fight the boss again, and can retry the fight if you didn't get what you were looking for, with the exception of the Final Boss, which is annoying since that day has three bosses beforehand. And, yes, as you may have feared by reading below, Reaper Beat and Taboo Minimimoto show up as Blue Noise as well. And, yes, you have to beat them on at least Hard in order to get all of the Secret Reports. And, yes, you still need to beat Minamimoto, the harder one, on Ultimate to complete the Infinity + One Pin Deck.
Unfortunately, some of these bosses were timed fights, so on your first time through, you won if you managed to survive for 30 seconds. No such escape clause in the post-game, and many of these bosses are still intimidating, even having killed the final boss.
Icewind Dale II has two of these, both within the same chapter. The first is a black dragon in the "Crossroads", which can be killed to close the teleport to Kuldahar. Players don't actually have to fight it, and can achieve their goal in a much easier way, but the difficulty of the battle alone makes it worth it for many players. The other boss is the Six Lost Followers, in the Kuldahar graveyard. This is regarded by many to be the hardest fight in the game, because A) there are six different enemies to fight at once, B) they are several levels higher than your party, and C) because each has only a few specific weaknesses, being immune to all other forms of attack, and with the weaknesses being different between each member. Victory gives the player the Holy Avenger, the best weapon in the game. Unfortunately, this pisses off quite a few people itself, as the weapon can only be wielded by a Paladin, meaning that there is no reward for anyone without a Paladin in their party.
Live A Live features several bonus bosses. The caveman chapter has King Mammoth, who offers a decent reward in the King's Fang, as well as the randomly dropped "Soda." The ninja chapter has two, one which offers a weapon that you can also get at the end of the chapter if you don't kill anyone, and another that drops an item that can deal a decent amount of damage if used in battle. The final chapter has about five, four of which drop the most useful equipment in the game.
Parasite Eve had a few in the Chrysler Building. While most of the bosses are color swaps of the storyline bosses, the giant cockroach and giant bee were exclusive to the building. The original Eve is at the very top of the building, and defeating her gets you a different ending.
Lost Odyssey has seven: Persona, King Kelolon, the Cave Worm, the Blue Dragon, the Holy Beast, Legendary Spirit Sorcerer Fu, and The Immortal One in the Backyard.
Players with access to Xbox Live can get a new downloadable dungeon with an extra boss Professor K, aka The Killalon.
Grandia Xtreme, rather than a new and unique boss, gave you the chance to go back to the old dungeons after beating the final boss, and in one of them you can fight a super-powered level 200 version of a boss you already faced.
Monster Rancher Advance 2 features Ragnarok, a wandering special Dragon who only appears after beating the final boss. He will only appear to fight you once a year, and only if you have a specific kind of monster on your farm. If you're not prepared to fight him on the week he comes to visit, too bad for you! His stats are extremely high (especially considering when your monster can first fight him), and he's tough.
In the dungeon before the Point of No Return, you are given the opportunity to fight the spirits of the three dragons you defeated. They drop some useful attack items, and they're also guarding chests containing powerful equipment.
There's also the Poltergeist-posessed armor set in Fort Magrad, an optional section of the Snowfield on Disc 3 (you travel through this area on your way to Velwebb. Hint: the sword has an instant-kill attack and it always uses it at the character who manages to dispatch it.
There's also the four Dragoon ghosts in Velwebb, and not to mention Magician Faust at Flanvel Tower, who is the most powerful enemy in the game. Beating him does get you a great reward though in the Phantom Shield along with 30,000 gold. Here's everything you have to go through to get to him, which definitely puts him in this trope by the above definition: Throughout the game, there is a side quest to collect a total of fifty stardust scattered throughout the continent. Every tenth stardust, when shown to the proper character, will give you a different item. The final item is a mirror that is required in order to face Faust. Faust is an insanely powerful Wingly who was second-in-command to Melbhu Frahma, but ends up being a dozen times more dangerous, possibly due to having been alive and studying/training for the entire time his "boss" has been asleep. You then have to find the entrance to Flanvel Tower, following a winding maze of teleporters just to get to the tower. If you do not have the mirror in your possession the first time you see him, he WILL kill everyone in your party with one blow a piece, and you will be unable to touch him. As it turns out, this first Faust is merely a projected image. The real Faust is able to cast his magic through the image even while being twice as deep in the dungeon. And so, obviously, you must finish the maze.
Riviera: The Promised Land has Hades, the boss who only appear in the extra content section after you complete the game and obtained the Key to Hell from the Zombie Dragon in chapter 6. His Breakout does heavy damage, but he only attack once every 3 of your each character's turns (estimated), so if you keep healing yourself with elixer and attack him, he's a pushover. Of course, the final boss can has its HP brought down by 53% with Fanelia...
All the Geneforge games have an 'Expert' level dungeon with the toughest Bonus Boss in the game. Most of them generate repeated creations to add to their attack power, and traps that deal extra damage unless the player has the skill to disable them or at the least reduce their effect. The worst is the Titan of Geneforge 4, which each time it was weakened to low health would shift to a new form, with a new set of attacks, defenses and vulnerabilities, requiring the player to have mastered a wide range of combat abilities. And of course, leaving the dungeon to rest also reset this Boss to its original form and strength.
Bahamut Lagoon has special "side quests" - essentially single battles - available throughout the game. One of them, appropriately named Hard Dungeon, is only available in the last seven chapters and is far more difficult than the final boss.
After beating Machinedramon and finishing the main story in Digimon World, you can continue the story and find a new level with high powered Mook Digimon. At the end is Machinedramon once again, only this time his health is maxed out at 9999 and his stats are also quite high. This is all for bragging rights.
While it's "only" a Mod, the Knights of the Old Republic Brotherhood of Shadowhas a flashback to Malachor V. You're pretty much stripped of all your gear, and have to re-create the single-combat against Mandalore that ended the Mandalorian Wars. Comparatively, the canonical Final Boss fight against Malak is nothing.
Mother 3 features several. First there is Lord Passion, who carries Duster's Infinity Plus One Shoes, Lil Miss Marshmallow guards a decent weapon for that point of the game, and the King Statue is just there for experience and is ridiculously easy if you know what to do.
The Doppelganger in the .hack//G.U. games is optional, but is ridiculously difficult and gives some of the most powerful weapons in the games.
The Xbox 360 game Blue Dragon has several Dragons that don't need to be beaten, but give the player a useful accessory if they are. Genuine Bonus Bosses include the Gold Mecha Robo, the King Poo, and the Golden Poo.
Dragon Age: Origins has several optional bosses among its many sidequests. The Revenants are powerful undead warriors that are managable on their own but get downright nasty with backup such as the ones that drop the Juggernaut equipment. Gaxkang the Unbound is an homage to Kangaxx from Baldur's Gate. Flemeth shapeshifts into a High Dragon. An actual High Dragon (who could be beaten easily if you surrounded it with Traps before you aggro). And many more.
Dragon Age II helpfully marks its bonus bosses with dedicated Achievements you get for offing them: a Varterral, a High Dragon, Xebenkeck the Desire Demon (who happens to be an old chum of Gaxkang from part one), and Hybris the Pride Demon. The last one is particularly bad news.
Resonance of Fate pits you up against Sullivan and Rebecca at the end of Neverland. Unlike many examples on this page, they are generally considered pushovers, especially compared to what you fought to get to them.
The Spirit Engine 2 has a variant: the bonus boss, Urtat Underval, is fought roughly halfway through the game rather than at the end. Another variant is that you fight him twice; once as a human, and once as a hulking zombie.
Ys VI: The Ark of Napishtim has Majunun, a blowfish-like creature that guards the Eldian Orb and will kill you in one hit the first time you can access it. Just finding it is a Guide Dang It, and to have a chance of winning at all, you need to nearly max out your EXP, which takes many hours, as all the enemies only give 1 EXP on the highest few levels.
Fossil Fighters has a huge slew of bonus bosses, one of which opens up before the final boss, and the rest of which appear afterwards, in the Playable Epilogue.
The lone bonus boss available before the game's end is Petey, a dino battler who demands to fight a team of three specific dinosaurs. If you take the time to grind those three specific dinos, he's managable, but if you're anything less than maxed, be prepared to hurt from it.
But after the final boss? Both Saurhead and the BB Trio reappear with "marathon battle" bosses, where you have to beat three of their teams with no break in-between. They're tough, and your reward is the Olympus Mons from waaay back at the game's halfway point. You can finally fight Dr. Diggins, though he offers up nothing but bragging rights (and EXP, if you're looking to grind). You can fight a samurai who's been in the hotel room next to yours for the entire game, whose most notable trait is that his Trainer rank is one beyond "Master." Oh, and if you're feeling lucky, punk, you can go back to the dinaurian spaceship and challenge Duna, Raptin, and Dynal—all at once. And that isn't even all of them!
The sequel, Fossil Fighters Champions, follows suit. In addition to almost all of the important characters having high-ranked teams you can fight in the Playable Epilogue, there's an entire bonus tournament that culminates in a fight against Rosie from the previous game. There were also DLC bonus bosses—including a strange character named Ryne, who gives you a new legendary vivosaur for winning, and Duna, Raptin, and Dynal again.
Fallout has had several of these across all the games in the series.
Fallout 3 Has five or six super mutant behemoths who you can hunt down. Admittedly, one is a Mini-Boss over the course of the main story, but even then, you could just skip the entire section. Other optional bosses include Commander Jabsco of Talon Company, Lag-Bolt and Enclave Squad Sigma in Broken Steel, and the three Ant Queens.
Fallout: New Vegas has the Big Bad himself, Caesar. Especially compared to his second in command, Legate Lanius, Caesar is pretty weak for a boss, only being about as tough as an Elite Mook. However, he's in the middle of the Legion's stronghold, and his personal section (the only one you're allowed to visit) is crawling with dozens of Legion troops. When you get past them, he is protected by eight Praetorian Guards armed with shotgun fists, each of which is as powerful as him. At lower levels, Caesar and his guards will usually dogpile you into a corner and beat you to death in a few hits, since said shotgun fists do ridiculous damage and Caesar and his guards are fast. However, if you go there at a later level with a good companion and high level weapons they'll go down easily enough.
The four (five with Old World Blues) legendary creatures in New Vegas, which are reskinned, upsized, and overpowered versions of their normal species. Admittedly, a sufficiently leveled character can make short work of most ( Legendary Cazadore, Legendary Nightstalker, and Legendary Fire Gecko) but the Legendary Deathclaw from the main game, and LegendaryBloatfly from Old World Blues can usually kill you in... Two hits. Almost always.
There's another boss Deathclaw in Lonesome Road, named Rawr. It's a Lightning Bruiser, even compared to the Alpha Male, and will kill most characters in one hit, although it has somehwhat less HP than the Legendary Deathclaw. Defeating him allows you to build one of the most powerful Unarmed weapons from his talons, Fist of Rawr. Or Fist of the North Rawr if you have Wild Wasteland! There's also Gaius Magnus and Colonel Royez, who are only available if you choose to nuke the Legion or NCR respectively at the end. The latter has all of his SPECIAL stats maxed out, the third highest HP of any human enemy after Ulysses and Legate Lanius, a Damage Threshold of 24, wields a plasma caster with overcharge ammo, and regenerates his HP very quickly from the radiation.
Baten Kaitos Origins gives us a few. There's Nasca, Valara, Heughes, and Wiseman, who are fought to tie up loose ends; one of them allows access to the game's True Final Boss. There's also Arma Prototype M, a.k.a. The Wicked Gawd, who is the final boss of the Coliseum and is absurdly hard.
In Alpha Protocol, the Blood KnightAction Girl SIE will offer to team up with you during the mission where you first encounter her. You can agree to the alliance, or you can attack her (or you can agree, complete the mission, then attack her when you encounter her again at the end of the mission). Not only will she not die when you win, but your rep with her will increase.
Xenoblade has 5 bonus bosses wandering around the world that are above the player's maximum possible level of 99: Final Marcus at 100, Ancient Daedala at 105, Despotic Arsene at 108, Blizzard Belgazas at 114, and Avalanche Abaasy at 120.
One long sidequest chain with its own story that covers almost half of the game leads to a bonus boss. Though this one is not overleved, it stands out because the boss is one of the NPCs the team has been doing quests for, Bana the Nopon, the battle is under a tune only reserved for a few select Hopeless Boss Fights, and the quests that lead to it can be Lost Forever.
Legend of Legaia has Lapis, who has insane attack power and can incapacitate a party member with a string of vicious attacks that deal upwards of 200% of the character's HP. Beating this boss requires either a lot of luck, hours of Level Grinding, or using a very specific accessory setup. note Specifically, equipping the Luminous Jewel accessory. Since Lapis's attacks are Light elemental (The game does not mention this.), using this accessory cuts his damage output in half and makes his attacks survivable.
Marvel Avengers Alliance has the Epic Bosses in certain missions, which only show up if you fight every battle and complete every deploy (which often require spending rare Command Points to recruit specific heroes) in that mission. The bosses offer stronger weapons and gadgets and higher chances of winning more Command Points as prizes for defeating them, compared to normal bosses.
Even an RPG that is stripped down to its bare mechanics also has one. Parameters has the bottom rectangle (previously the second-strongest enemy in the game), which turns into a 9999 hp opponent with high defence and attack after beating the Final Boss. Thankfully, it isn't really that difficult so long as you have enough life regeneration, but it does get tedious as it regenerates health quickly and can take a ton of punishment.
Morrowind has an Anyone Can Die nature, so naturally, anyone in the game can be fought and killed. But special mention has to go to Vivec. You are not required to fight or kill him during the main game or either expansion, but if you choose to, you'll have a hell of a fight on your hands. Bonus irony points if you soul trap him in Azura's Star.
The Ash Vampires are another example. You only have to fight one in order to get an item off of him, but there are 6 others you can kill. Each one you kill is supposed to weaken Dagoth Ur when you fight him, but this does not work due to a glitch in the calculation system. You only need to fight the if you are going for 100% Completion or for their somewhat useful enchanted items.
Erandur-Vangaril (a lich). He can only be found in a specific cave that none of the game's quests lead you to, and can only be fought there once your character reaches a certain level.
The giant slaughterfish, who shows up in one of the dungeons you explore in the Thieves Guild questline, but chances are you won't ever see this one if you don't fully explore the place.
There's also the Uderfrykte Matron at Dive Rock.
The Dragonborn DLC of Skyrim has the Ebony Warrior, who challenges the player once they reach level 80. His equipment is heavily enchanted, has 50% damage resistance to all elements and can use Dragon Shouts.
There are also a few named dragons which are not required to be fought. Of particular note is Vulthoryol, who can be summed by using the Unrelenting Force shout on the orange globe in Blackreach.
The Last Story has Therius and Gigamuruk. The first is a one-on-one Duel Boss who can only be challenged with Zael alone, in a callback to an earlier boss fight. The latter is fought at the conclusion of the game's running Tournament Arc.
The sequel has even more of these, most of whom are based around chess pieces. Each of the four Caves of Darkness contains a different variation on the Knight, and each one is progressively more difficult—especially because the Caves are timed, and even though you can keep battling if you run out of time, if you do, you'll be kicked out of the dungeon before you can collect your rewards for completing it. There's also a Pawn who you have one required fight against early on—but he keeps getting stronger and stronger throughout the game, and you can return to challenge him after different story events. The last two sets are linked—the "big" Bonus Dungeon ends with a fight against the Demon Queen, who serves as a combination of this and a True Final Boss. This unlocks the Bishop, King, and Queen, who fight you back to back in a Call Back to the original game's final boss.
Tyrant in Opoona. He can actually be fought surprisingly early on for an example of this trope—before the game's halfway point—and defeating him is required to raise your friendship with a few NPCs. However, taking him on so early and surviving is another matter entirely.
Robopon has a couple. In the original, you can rematch the first six Legends in Zero Tower post-credits. The second game has several, including Rena's restored-to-youth mother, the younger version of Nick D., the Robopon in Delica Castle's basement, and the W-King.
Shoot Em Ups
Gradius Gaiden has one, in a way. Normally, on Stage 8, you face six bosses, but play it on the second loop of the game to face a seventh: the Beam Spammin' Heaven's Gate.
Always present in Touhou games ever since Story of Eastern Wonderland. The fans would probably riot and destroy Tokyo if ZUN ever released a "proper" Touhou game without one.
Perfect Cherry Blossom had an extra Extra Stage with an extra Extra Boss. She's the one that made Gensokyo. Frightened yet?
Lampshaded in the 11th game, Subterranean Animism. When playing as the Marisa/Alice combo, there's a conversation along the lines of: "Why are we here again? We already beat the final boss." "It's the Extra Stage, just do it."
Hellsinker, as with Batrider and Garegga, has loads of secrets. Defeating the Scarlet Queen will result in a secret form of the boss that unleashes hell for 15 seconds, then disappears. The secret form can be easily triggered if the player has the game at a high rank, but it can also cause quite a surprise by randomly appearing under normal circumstances. If that happens, you're in for a world of hurt.
Lots of missions in the Ace Combat games feature enemy aces whose defeat is not necessary for mission completion. Unlike traditional examples of the trope they're not really harder than the compulsory aces. On the other hand, there is a more traditional one in Mobius One and his Raptor, who would be encountered in an Ace difficulty run of the Gauntlet if you did well enough. Similarly are Scarface One and ZOE Commander in a certain Skies of Deception mission.
Two of them are available in the combat sequences-filled Dating SimMitsumete Knight : Zeelbis the Bloody and Salishuan the Spy of the Eight Generals of Valpha-Valaharian, the main enemy squad of the game. While not a storyline-related boss unlike the other two, Sparkster of the Rocket Knight Adventures series count too.
International Super Star Soccer Deluxe for the SNES introduces a bonus match against an All-Star team with perfect stats after you win the World Series. Not only is this team supremely talented, but all your players are tired or very tired.
In Konami's NFL Football for the Super NES, you can enter a code to play against the Konami team, who have A+ in all stats.
Most of the bosses in Dead Rising are Bonus Bosses. And the handful you do have to fight to complete the game are all That One Boss. The game is hard.
Technically you don't have to do any of the bosses. To finish the game you just need to be alive when the time runs out. You only need to do the quests if you want Ending A.
Fatal Frame has a particular optional boss only on the Xbox version. A samurai ghost named "Armoured Warrior" who only appears on the final night on the hardest difficulty, who can instantly kill you if he touches you AT ALL. Oh, and he's fully invisible too.
And he can't be pushed back with a critical shot like every other ghost can be so he's ALWAYS coming towards you without stopping. Again, being invisible, you can't see him but rather HEAR him, unless you get a shot of him fading in and out quickly while looking through the camera, which is the only real way to defeat him.
Third Person Shooter
Lost Planet: Extreme Condition features a Bonus Boss, but it's rather unusual. Relatively early in the game, you encounter a giant worm, Akrid, that can CONSUME YOU and takes a massive amount of damage before falling. You're expected and encouraged to run from it... but if you want the challenge, you can fight and beat it, effectively making it a Bonus Boss. There's even an Achievement for doing so. Later on, you can fight a giant Akrid moth.
Turn Based Strategy
Fire Emblem: Radiant Dawn has Levail, General Zelgius' apprentice. While Ike fights a Duel Boss battle with Zelgius, the rest of your team takes on Levail and his army. Defeating Zelgius is all that you have to do to beat the level, and the rest of your troops don't even have to move, let alone fight Levail (who as a top level Sentinel equipped with the Wishblade is one of the few genuine threats you'll meet in the last quarter of the game). Many choose to engage him though, out of the desire to kill a few more opponents and maybe get their hands on The Wishblade.
Levail's predecessor as wielder of the Wishblade, General Bryce of Daein, is another Optional Boss. Appearing in the last level of the game, Bryce stands in the centre of the map, astride the easiest path to the Final Boss, Mad King Ashnard. It is however, entirely possible to avoid fighting Bryce by taking another route, although most players don't think to do so.
In Genealogy Of The Holy War, in the Final Chapter, Areone is flying around with a squad of Wyvern Knights. However, the chapter can be cleared without ever fighting him, and he'll even become an NPC ally if Altenna talks to him.
Outside of DLC, there's Spotpass character Priam, descendant of Ike. His map has you field 30 units, which is essentially your entire roster and one of the highest unit counts in FE ever. Priam himself is equipped with three Breaker skills, Sol, Luna, and nearly maxed stats making him quite a challenge to defeat.
Demon Supreme Overlord Baal in Nippon Ichi's Marl Kingdom series, La Pucelle Tactics, Disgaea, Phantom Brave, Makai Kingdom, and Disgaea 2. In fact, most Nippon Ichi games let you fight characters from their other games as bonus bosses, and they're always at obscene levels. Laharl, Etna, and Flonne from Disgaea: Hour of Darkness are all Bonus Bosses in Phantom Brave, for example. In many cases, defeating them will recruit them into your party. While the final bosses of the games tend to be at level 90-100, the bonus ones usually start somewhere around level 1000. That's start mind you. In "Etna Mode" of the new Disgaea PSP remake, Baal is literally level 9999.
Mind you, that's not all that impressive. He's actually the third level 9999 boss you've fought by then. He does, though, have about 3 or 4 times the stats of the last one, on an area that randomly clones one character a turn (friend or foe, but clones are all foes), triples all enemy stats, stops all special abilities, and prevents lifting.
Special mention should go to his Disgaea 3 DLC. Max level, three copies of his Tyrant form (as shown in the page image), well over 400 million HP, and an evility that nulls out damage each round based on how many copies of himself there are on the field. If you don't act quickly enough, the enemy base panels in the back will summon more Baal copies. If you're still too slow, they'll start bringing out Omega Sentinels for the Baal clones to Magichange with. Either you finish it quickly, or otherwise you're screwed.
Disgaea adores this function. The final story boss of the game is often one of the absolute weakest enemies the game has to offer. Disgaea 2 had, alone, Overlord Priere at level 500, Marjoly at 1000, Overlord Zenon (the real one) at level 2000, Overlord Baal (the first round) at level 4000, and you still have quite a lot of others. The re-release (mentioned below) also added the DLC characters whom are easy to beat but all sit at 100, and three characters form Disgaea 3 starting at level 500 and ending at level 3500. Additionally, the final boss of Disgaea 2 is level 90 and has no geo effects on the field and is alone. The bonus bosses are often not that gracious, and may have backup, geo effects, and ridiculous levels.
Phantom Brave and The re-release of Disgaea 2 brought back Mythology Gag Pringer X as a Bonus Boss, and he's more dangerous than Baal up there for a good reason: he can become immune to any special that's already been used against him, meaning you can't spam the same attack over and over, you HAVE to round out your move set. Later on, you get the chance to fight Eight of them, and they will all become immune to any special used against one of them, but that's not all: You can later pass a bill that turns all of the Land of Carnage monsters from Uber to Uber Lord, making them not only stronger, but you can't capture them and the bill sticks for that cycle. If you go back to take on Pringer X's army again, their stats are maxed out at 40 million, meaning damaging them is a daunting task in and of itself, much less hitting them.
Disgaea Dimension 2 has an incarnation of Baal that is at the moment, the absolute hardest boss NIS has ever made. Most of the examples of this trope in their games can be taken down easily if the player level grinds enough, but Baal in this game, even characters with maxed stats will struggle with him. He never loses a stationary attack bonus, so his damage goes up every turn, switches between some abilities throughout the fight that include summoning clones of him every turn that will rack a ton of damage if you don't kill them, having 50% of all attacks miss, and destroying you base panel and healing himself at the end of ever turn, but throughout the whole fight has Pringer X's ability to become immune to special attacks after they're used on him (though he loses immunity to attacks he was hit with previously when he changes evilities). He has so much HP that it's basically a requirement to raise the stationary attack bonus as high as possible to take him down and even then he's still a Marathon Boss.
Luminous Arc 2 has the reoccuring boss for the optional That One Sidequest Spa Battle series, Vanessa. Not only does she have high strength and can use a stat-boosting spell, she's also joined by respawning and stat-specialised Kopins, who only exists to wear down your party. Pity the unfortunate player who didn't bring any anti/nulling fire Lapis and suffers from either her attack, spells or Flash Drive. She'll get stronger each time you face her, until the sidequest is finished. Beating this multiple of times with New Game Pluses is required for the 100% Completion.
While not really a "Boss" per say, the original Advance Wars has a bonus Mission after the Final Battle with Sturm called Rivals, where Eagle challenges Andy to one last go around. In order to access it, you have to play through the Campaign and choose Sami for every Green Earth Mission (barring Eagle's introduction early on of course). This is noted to be quite difficult, as Sami's Green Earth Missions are easily the hardest of them (it doesn't help that she's not nearly the terror that she is in later games either), but it pays off in more ways than one; not only does it give access to Rivals, it also places Eagle as the 3rd CO in the Final Battle, along with an entire squadron of air units to start off (considering the closest airport is neutral and well near the middle, this is a HUGE plus). On the flip side, if you play Rivals in the already painful Advanced Campaign, you're basically doomed to be playing the map for a long time.
Wide Open Sandbox
Both bosses in Minecraft are optional. The first is the Enderdragon, which doubles as a final boss. The second, more traditional example, is the Wither, which has to be summoned by completing a difficult task, is insanely hard, and drops the Nether Star, which can only be used in constructing Beacons, devices which give you bonus abilities.