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Bosses in this game rarely pull any kind of punches, but while some are distinctively easier to beat with a well-thought out roster, others are much, much trickier.

NOTE: As they are intentionally designed to be extremely difficult, the final bosses of the Refraction Railway cannot qualify.

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    Main Story 
  • Being the Final Boss of Chapter 3, Kromer is appropriately pain-inducing to beat. Right off the bat, her first phase has no damage weaknesses and in particular resists Blunt, which can be a nasty shock since most of the enemies in the chapter and dungeon are weak to Blunt instead. Then, she has a passive that gives her a huge heal and attack buff if she has any Bleed or Burn on her at the end of the turn, which can No-Sell an entire turn's worth of effort and renders the Kurokumo, Liu, and N Corp. Identities useless. Gameplay and Story Integration also bites you hard if you bring Sinclair along and don't have a full collection of the dungeon's specific E.G.O gifts, as he will take a huge performance debuff without them. Clashes against Kromer, if lost, will have her do disturbing amounts of damage and/or nail stacking that can stagger a squishier Sinner in a single combo. Furthermore, at regular intervals, she'll use an attack that instantly Staggers the targeted Sinner and makes them take double damage the next turn on use, after which she'll fire all of her attacks at them (several of which are her 4-coin Purification attack) and force you to redirect every attack to avoid their almost-certain death. The only consolations are that you can deal some serious damage if you win the clash against her "I Shall Claim Your Life!" skill in the first phase to instantly stagger her, she'll start taking and dealing double damage past a certain point in the fight to let you bring the hurt, and if you manage to reach her second phase with your team relatively intact, the fight becomes far easier; while she can still bring the hurt with some powerful attacks, she actually has weaknesses to Wrath and Pride affinities as well as a Fatal Pierce weakness on her Maw part, will periodically drop her defenses further when going on the attack, and and can similarly be forced to Stagger if you win a check event after dropping her health enough, making her much squishier.
    • She, too, was hit with the Nerf bat at the start of April 2023. Now, by collecting the "A Sign" items in the dungeon, you can reduce Kromer's regen and power gain all the way down to zero. There was a glitch that made it so it didn't work in the second phase, but that's since been fixed, making her much more manageable for anyone running the aforementioned groups of Identities.
  • The penultimate battle of Canto V's dungeon against the trio of Ahab, Queequeg, and Starbuck is generally considered the hardest encounter of the dungeon, and much harder than the fight with GasHarpoon Ahab immediately afterwards. You're pitted against three foes with scarily powerful rolls and stats, and are forced to start combat at 0 SP while Ahab applies massive SP boosts to her side, letting them consistently flip heads and outroll your clashes by the second turn. While Starbuck has incredibly damaging attacks and is liable to one-shot Sinners on a direct hit, he's also pretty squishy and easy to stagger or kill if focused down with Piercing damage. The problem arises with Queequeg, who is not only extraordinarily tanky, only staggers once at about half health, and has an Auto-Revive in stock, but will frequently gain a buff that causes her to pull all attacks targeting Ahab to herself instead, rendering them unclashable. The buff can only be disabled by cracking a fairly tough shield she puts up when drawing aggro, and disabling it only takes effect on the next turn, meaning that without some Evade manipulation, Ahab will always focus down one Sinners with up to four one-sided attacks and obliterate them without any way to fight back, turning the fight into a frantic DPS race to kill the trio before your Sinners unavoidably die one by one. Woe betide you if Starbuck isn't dead by then, as he'll also gain a buff that lets him perform another unclashable follow-up each time Ahab attacks, which can be disastrous considering how hard he hits already. Killing Ahab instantly ends the fight, but it's easier said than done even without Queequeg taking aggro for her, as she has fairly strong moves of her own, high-rolling evades to waste your attacks, and can fully heal herself once if she's brought to half health, upon which she Turns Red and becomes more aggressive. On the bright side, Ahab is is fairly squishy and easy to stagger if you can get past her wall of defense, meaning that a savvy player can disable her before handling the other threats, which will also prevent her from activating Assist Defense.
    • Ahab and the trio return in Refraction Railway 3, and although the player gets to start off with more SP, the fight is just as hard if not moreso - a wave of Pequod Town Villagers is added before the actual to soften you up and stall for time (although also serving as a good source of SP and resource farming), and all of the bosses have considerably higher stats than their story encounters, meaning those one-sided attacks are going to hurt if you can't land a stagger beforehand, which in turn is also harder because of their increased HP and Defense Level. Furthermore, you have to ensure you leave the fight with an intact and healthy team, since you'll have to contend with a buffed GasHarpoon Ahab immediately after the trio without any time to rest.
  • Kurokumo Clan Captain Jun from Intervallo 5.5 can be a severe pain in the rear, and for many was far harder than the actual Final Boss fight against Distorted Kim. To start off, he comes at the tail end of a 2-wave encounter with other Kurokumo members whom, while serving as a buffer to generate SP and Sin resouces off of, also have fairly high-rolling moves and Bleed stacking that can whittle down a team that gets unlucky with clashes. Then Jun himself shows up, packing far higher stats than his henchmen, passives and pages which let him stack up alarming amounts of power and damage buffs, and even higher damage and Bleed output, along with a passive that lets him gain extra actions whenever his allies are defeated. His action economy is also scarily good, starting out with two moves and will steadily gain a slot until he maxes out at 5, meaning he can become increasingly likely to launch one-sided attacks if his minions are not dealt with fast enough. He also comes packing Rules of the Backstreets, a powerful counter which can roll up to four coins depending on how many allies he has active (and thus will always be at maximum power on the first few turns), and Sky-clearing Cut, a nuke of an attack that can hit two targets if the main one has enough Bleed, deals a ridiculous amount of damage if it connects, and gains 5 power if he's using 5 or more attacks that turn. The worst part is that since his fight is a non-Focused encounter, not only are your Sinners likely to take deadly one-sided attacks from the enemies outnumbering their actions by the second wave, the player has little to no control over Sinner targeting, meaning that it's nearly impossible to stop an effectively random Sinner from taking a full-power counter that will potentially stagger or kill them (especially if a Sinner's target dies and they automatically retarget Jun); the player doesn't even get a Morton's Fork scenario where killing Jun's allies powers up his Sky-clearing Cut while leaving them alive powers up Rules of the Backstreets, because they have no control over how they kill his allies anyways, making the only real solution to just bring Slash-resistant and high-rolling Identities and pray for the best.
    • To make matters worse, he can show up as an encounter in the event dungeon (albeit one that is easily seen in advance, as it's the only Risky encounter that ever shows up), which throws you right into the fight without an initial wave to build up SP and action slots on, which can result in a swift demise if it was at a point where your Sinners don't have enough SP to outroll him and his goons.
    • You can also encounter him in a Mirror Dungeon run during his event (which allows B.L. enemies and bosses to spawn as uniquely marked nodes), and not only will he benefit from any enemy buffs you've taken along with the general stat inflation of the dungeon, the fog of war in Hard Mode means you may not see him coming until you're railroaded into his encounter. Woe betide you if you find him on Floor 4/5 on Hard Mode, as not only can you expect his stats to be doubled and his rolls (along with those of his minions) to be absurdly high considering their already high base values, it's still a non-Focused encounter, which can potentially end the run right there as his counter can be an unavoidable One-Hit Kill if luck isn't in your favor.
  • The Climax Boss of the second part of Canto VI, Mirror Heathcliff is effectively a dungeon boss that has to be fought during normal story progression. This actually causes significantly more problems than you'd think, as Heathcliff has a massive HP pool, high rolls, resistance to all three damage types and unique mechanics, while your Sinners start the fight with 0 Sanity and no E.G.O. resources or any other kind of collectibles that help you. The boss itself starts with 15 Sanity, and as a result the first few turns effectively boil down to a Luck-Based Mission because they can easily snowball over your Sinners in terms of Sanity due to gaining a big chunk of it every time they win a clash, and having their conditions to lose SP being much more hard to accomplish. This is complicated even more by Mirror!Heathcliff's gimmick; he only targets the original Heathcliff and wins the fight if he dies. If you're particularly unlucky with speed die rolls, the fight can end in an instant because Mirror!Heathcliff will outspeed your team and blitz Sinner!Heathcliff down, something particularly troublesome later in the fight when he starts using attacks that can only be clashed by Sinner!Heathcliff. If your Heathcliff gets staggered or Corrodes even once, the fight is practically over because those attacks become completely unavoidable, and they will inflict so much Bleed that even if he survives the initial hit he'll be dead next turn. While Bind and Haste support can help with keeping Mirror!Heathcliff slow enough to redirect his attacks, this is not something that can realistically be fueled every single turn, and even then that does not defang his brutally high damage that can easily cut down your defenses. It's practically required that you bring massive amounts of Sinking and beefy Identities that are of a relative speed (which are far and few between) to redirect at least some of the attacks and pray you get good flips on the first few turns so you can keep Heathcliff on as little Sanity as possible and have some chance to actually build up resources. And even then, one bad turn can end the fight immediately.

    Mirror Dungeons 
  • If there's one boss that everyone fears during Mirror Dungeon 1, it's Headless Ichthys: it has a bunch of health, can do far more attacks in one turn than you can, and hits HARD using attacks with very high coin power and various debuffs like Attack Power Down and Bind. It can easily win clashes if the RNG favors it enough to let it roll heads, and the debuffs on hit can snowball if you let them stack, allowing it to destroy even a well-equipped party, doubly so if they're weak to Blunt. By contrast, its fellow Mirror-original boss Abnormality, the Alleyway Watchdog, is a considerably easier fight. It used to be even worse if you encountered this thing in Monday's Thread Luxcavation dungeon, as you would be going in with 0 sanity and without any buffs or helpful items you may have had encountered in Mirrors.
    • Luckily, the Thread Luxcavation iteration of the fight was hit by the Nerf bat by the end of March 2023. In addition to performing less actions, its speed was also dropped so that its attacks became easier to intercept. Its most powerful attack was also changed to not being used twice in one turn when it was used - whenever it uses it now, it is the only attack it will use in the patched version. Unfortunately, there's no such luck if you encounter it in a Refraction Railway or later Mirror Dungeon, where it not only behaves just as it did before the nerf, its stats are even higher to match its new point in progression, although you'll also have a bigger team of 6 or 7 Sinners instead of the 5 you had in Mirror of the Beginning.
  • Most of the Final Bosses of Hard Mode Mirror of Mirrorsnote  can be nightmarish due to the ridiculous stat inflation that all enemies get on the fifth floor, but two of them are particularly infamous, to the point where one of the most common "strategies" for those two (and to a lesser extent, the Floor 5 boss in general) is to just quit the dungeon on the node right before the boss, as it only incurs a very minor XP/Starlight loss while saving potentially 30+ minutes of pain..
    • My Form Empties, while not as annoying in Refraction Railway due to being a Puzzle Boss that, at worst, required some resetting for players trying to get an optimized clear time, quickly became loathed when encountered as the final boss in the Hard Mode of the second Mirror Dungeon. MFE as a boss is centered around winning clashes against its accompanying miniboss enemies to slowly build up Karma on them, which kills them at a high enough amount, after which MFE itself is open to proper damage. The problem arises from the nature of Hard mode - enemy stats, even on Mooks, are inflated to very high levels, and will generally demand a powerful skill at a high SP to clash against, if not an E.G.O outright. This similarly applies to bosses, meaning that in order to win clashes against MFE, it is nearly required to use E.G.Os against almost every attack, and because the heavily inflated stats make players unable to use brute force to kill a miniboss in one turn like in Railway, the fight effectively turns into a Marathon Boss as the player is forced to play by its rules. The end result is that the fight comes down to how many E.G.O resources a player is able to stockpile beforehand or if they were able to snag a Gift that generates resources, as they will need to use multiple E.G.Os every turn in order to safely beat MFE's clashes and eventually win. In the worst case scenario, a player is liable to run out of resources halfway through, which is very much possible due to so many previous enemies similarly needing liberal E.G.O usage to safely defeat, and be left much more vulnerable to losing clashes and ultimately lose due to the Karma buildup on their Sinners. At best, the fight is an extremely tedious and drawn-out process of slowly whittling down all the enemies due to the fight's design. At worst, the fight is a nauseatingly infuriating and borderline unfair battle that can make the entire run feel like a Luck-Based Mission if a player ran into a few too many bad fights or were unable to find a resource-generating Gift or two.
      • MFE returns as one of the possible final bosses of the Hard Mode of Mirror of the Lake, but all of the Lured minions now conspicuously have only a third of their health in Mirror of Mirrors, making it much easier to burst them down and kill them to skip phases of the fight, along with Mirror of the Lake also generally giving the enemies less extreme stat inflation compared to Mirror of Mirrors unless you took some particularly nasty enemy buffs. It's still a hefty challenge, but not nearly as bad as it used to be.
    • In addition to My Form Empties, we also have the Brazen Bull as a possible Floor 5 boss. The Bull was already arguably this to begin with due to its abnormally high rolls, massive HP and defenses,note  and extremely low stagger thresholds, all of which are dialed up to ridiculous levels with the enormous buffs the Mirror Dungeon grants it, making it an incredible statstick that eats damage like no tomorrow and spams nigh-unclashable attacks that can overpower even HE-level E.G.O.. It only becomes vulnerable after you've weathered its attacks for long enough, upon which it's most likely stomped half your team flat and put a strain on your SP and resource reserves. Even if you can survive the assault and break its head, it'll likely still have a good stock of HP in reserve to wall you, and it will still likely be able to outroll you even with the passive that permanently reduces its attack power by 3 after its head is broken.
      • Brazen Bull returns in Mirror of the Lake, and it shows up on Floor 4 instead of 5, meaning that skipping it and claiming your slightly reduced rewards is no longer an option in the Hard version of the dungeon. Although it likely won't be as buffed as it was in MD2H due to the potentially lower power buffs and lower scaling on Floor 4, it rolls as horrifically high as ever while being just as durable, so you best hope you didn't take any particularly nasty enemy buffs and have taken full advantage of all the new buffs you can leverage in the third dungeon.
  • Guido and his minions can show up as the Floor 1 boss in Mirror of Mirrors and Mirror of the Lake, and are generally much tougher than anything else you can get as your first boss in either. Although you're likely way stronger than you were when you fought him first, they're appropriately leveled to match it and generally show up at a time where you probably don't have much SP, collectibles, or Sin resources to fire E.G.O. with. They're particularly bad in Mirror of Mirrors - Hard, as they'll take advantage of the substantial buffs enemies get on Floor 1 combined with their high base stats to outroll your Sinners and cause some major damage. Meanwhile, Mirror of the Lake lacks the early buffs even on Hard Mode (which instead makes them slightly higher level), but Guido now comes with five Inquisitors instead of four while starting with two actions, meaning that they'll always outnumber your actions and be able to score cheap attacks unless you stagger them fast, and will be guaranteed to land at least one attack on the first turn.
  • With My Form Empties being hit with the Nerf bat, Dream-Devouring Siltcurrent quickly rose up to take its place as what is likely the toughest Final Boss in the Hard Mode of Mirror of the Lake. It packs a boatload of health and innately powerful rolls boosted further by the accumulated enemy buffs on Floor 5, and will inflict 1 Paralyze to all Sinners at the start of each turn until you break its Fluorescence; E.G.O. is already practically mandatory to outroll its boosted clashes, but now not only are all plus-coin clashes crippled in general, E.G.O. will always roll tails and most likely lose unless it uses negative coins, upon which Siltcurrent will almost certainly stagger or kill the target with its extremely powerful moves. Fortunately, the fight gets easier if you can repeatedly break its Flotsams to redirect its Blind Obsession attack, but since there'll always be at least one turn where no Flotsam is present, someone will have to either gamble on outrolling it with a Paralyzed E.G.O. or sacrifice a major chunk of HP to take the hit, if not their life, not to mention the player also having to deal with Siltcurrent's other attacks while making sure one Flotsam is destroyed per turn. On top of that, Dream-Devouring Siltcurrent will always use an unclashable AoE attack that hits the whole party on the first turn, which normally does very little besides setting up its unique battlefield hazard, but with the Mirror Dungeon buffs now becomes a legitimate burst of cheap damage that can leave Sinners staggered and helpless on the next turn.

    Refraction Railway 
  • The Ardor Blossom Moth from MirrorClock OrangeRoad can be best described as an unholy fusion of the already difficult Ricardo and Skin Prophet, combining the former's insane bulk and clashing power (with Ardor Blossom Star being able to roll over 30 depending on how many Wrath skills it's slotted the turn it uses it) with the latter's ability to stack so much Burn on the Sinners that the fight effectively becomes a Timed Mission. The only way to stop its Gathering Steam abilities are to break its Wings to dispel all of its Ember, but this is made difficult thanks to the Wings being surprisingly beefy and the boss giving you as few as two or three turns to break them before it uses its strongest moves, not to mention that it can restore them not long after they're disabled, starting the cycle again. Like with Ricardo, the best option when dealing with it is to simply forgo clashing in favor of nuking it down as quickly as possible, as trying to counter all of its attacks simply isn't worth the resource cost to do so - and due to the amounts of Burn it can stack (with much of it being unavoidable due to it having some attacks that either inflict Burn on use or are unclashable), even this approach has barely any room for error. Furthermore, its position in the actual line also deserves mention, as it's placed after the battles with the Ambling Pearl and the aforementioned Skin Prophet, both of which specialize in heavy amounts of near-unavoidable Damage Over Time that will likely weaken your team for the Burn fiesta if you weren't packing strong healing abilities, although thankfully you do get a checkpoint right after beating Ardor Blossom Moth.

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