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  • Alternative Character Interpretation: Sigurd's uncharacteristically hostile sounding words when he left Solaris in Ramsus' flashback seem somewhat out of character for Sigurd, given he was friends with Ramsus, and left due to finding his methods no better than what they were changing, and also getting free of the Solarian brainwashing. Was he being hostile in a Cruel to Be Kind way, making it seem like he was a jerk to make it easier for both himself and Ramsus to move on? Was it just a lie to cover up why he really left so as to not draw attention? Was it possibly even just Ramsus' own views of the conversation, thus making him an Unreliable Narrator? Sigurd later comments he didn't really mean to hurt Ramsus, suggesting it may just be Ramsus' view of the conversation, but it still leaves it up for debate how accurate it was.
  • Angst? What Angst?:
    • Billy finds out that the Ethos are secretly evil kidnapping murderers and his whole religion is a lie. Billy is upset by this for about a sentence.
    • Part of this might be due to the rushed nature of the second disc, which might have led to more scenes of appropriate angst otherwise, but none of the cast are that upset over almost everyone on the planet getting killed. Billy lost an orphanage, Rico lost a city, Bart lost an entire kingdom of people who adored him, but all they are worried about is saving Elly.
  • Anti-Climax Boss: The Post-Final Boss, Miang, or what's left of her, is pathetically easy. Granted, there are reasons for that...
  • Ass Pull: Bart "finds some documents" off screen that tell him the Administrative building in Nortune is really a gigantic Gear, which Bart pilots just in time to fend off the Solaris war machine.
  • Big-Lipped Alligator Moment:
    • At the end of Fei and Bart's fight with Ramsus, Margie summons a horde of rats to "cover" their escape. It works but it never happens again in the story, and nobody except for Ramsus comments on the randomness of Margie summoning the castle's rats to let her escape, which made it feel like it came out of no where.
    • When Fei gets into Solaris, he runs into an NPC that looks like Timothy, but isn't, and after the character confusedly asks who that is, the game continues as if it never happened.
  • Camera Screw: About 95% of screens give you 360 degree rotation of the camera, but some rooms have predetermined angles for when you enter a room. It's possible for the same direction you used to enter a room will cause you to backtrack.
  • Catharsis Factor: You know Uroboros, that ridiculously weak Post-Final Boss that Krelian tosses into the ring against Xenogears? That's Miang, or what's left of her. Unlike the rest of the game, she has no tricks up her sleeve, nowhere to run to, and no way of stopping Xenogears from going into Hyper Mode and paying her back for all the pain she's caused. Have fun.
  • Common Knowledge:
    • Xenogears, Xenosaga and Xenoblade Chronicles are NOT the same franchise. While it's true that they share creators, Mythology Gags, and many highly similar narrative elements due to the fact that the latter series are explicitly Creator Driven Successors of the first, and were written in such a way that many of them could have plausibly lead to story beats in one of the other franchises, they are separate IPs, owned by three separate companies (Square Enix, Bandai Namco, and Nintendo respectively), with three separate narratives and continuities that generallynote  do not cross over with each other (a bit like the System Shock and BioShock franchises, for instance). Even if they could be in the same setting, the fact each series is owned by a different company makes it very unlikely to be true, Xenogears especially because it was made before Monolith Soft became a thing, hence why the title only appears in Square Enix owned media. This is not helped by the fact that fans of Monolith's work tend to refer to the games collectively as the Xeno franchise for the sake of brevity, which can be misleading for casual observers and newcomers.
    • Quite a lot of confusion and misinformation exists among English fans regarding various plot details of the game's story, due to a combination of the game's own translation issuesnote  as well as access to Perfect Works and its English translation having been very limited for a long time. As such many fans assume incorrect things such as Citan having fallen for Yui after she defeated him in a sword duel (when it was actually her grandfather he dueled) or Abel activating the Zohar on the Eldridge and causing the ship's destruction (when the scene of him making contact with the Zohar took place back on Miktam04β).
    • A common rumor persists that the infamous budget cuts that disrupted the game's development were caused by Square assigning most of their resources to Final Fantasy VIII, while in fact the real reason is that a lot of inexperienced team memebers were unable to meet the deadlines set by executives, so a compromise had to reached, resulting in the final product being in this state.
  • Complete Monster:
    • Miang Hawwa is eventually revealed to be the true driving force of the game's conflict. Initially Ramsus's wallflower assistant, Miang turns out to be an ancient being with one goal: to prepare humanity for harvest by Deus. The "Eve" of the world, its first woman, Miang has helped to manipulate human history by running an Ancient Conspiracy, causing countless wars and conflicts with countless deaths. Miang demonstrates nothing less than cruel satisfaction at her manipulations, rubbing it in her lover Ramsus's face how he was a failed prototype of Ramsus's rival Fei to break his already fragile mind. Miang awakens Deus and causes the genocide of almost all humanity, in addition to having made it her personal mission to destroy the happiness of lover Fei and Elly's past incarnations every time they reincarnate.
    • Bishop Isaac Stone (originally Stein) is an agent of Solaris and one of the darkest and cruelest villains in a game full of soldiers fighting for honor and their beliefs. Having long ago murdered Raquel, the mother of Billy, all because she chose Jesiah over him, Stein continues the conspiracy of the Ethos by taking in orphans and lost people, only to send them to Solaris to be experimented for their secret weapon, and killing any survivors who became Wels or Reapers by sending out priests who he tricked into believing him. After the Ethos tries to break away from Solaris using weapons they found inside an ancient ruin, he begins to massacre them, leaving very few survivors. After being caught up by Billy, a young man who was devoted to Ethos, he gives him a Breaking Speech by telling him the monsters he killed were actually people that Solaris mutated.
  • Demonic Spiders: Tears, encountered in the Shevat maintenance tunnels, are incredibly annoying and terrifying enemies to fight. They always come in pairs, are fairly fast (often being just below Citan in speed), and hitting decent hard. What makes them a threat though is that if you kill one, the remaining Tear buffs it's damage, and starts using a multi-hitting attack that can instant drop anyone from full to zero in an instant. Between those factors, and being fast and easy to miss, they can potentially wipe your team out.
  • Estrogen Brigade: As discussed by Tetsuya Takahashi in interviews, Xenogears ended up finding an especially strong following with female fans due to the game's heavy psychological themes and characters with rich and complex personalities.
  • Event-Obscuring Camera: A number of non-secret exits can be completely obscured at any angle, or require turns that are unclear due to the position of walls.
  • Fanfic Fuel: It's eventually revealed that Miang can continually awaken in any woman after being killed and we only ever see a handful of incarnations of her out of almost a thousand from a period of almost ten thousand years, it can be fun to imagine what she did in the rest of her lives that weren't shown and how they impacted the world of Xenogears.
  • Fanon:
    • The strategy guide gives Emeralda's the surname "Kasim" after her "father", Kim Kasim. Despite it not being something that is stated in game or by the developers, fans frequently do instead, largely because she more or less is Kim's daughter, something the game itself basically states in a optional cutscene near the end of the game.
    • During the game, Krelian appears with blonde-colored hair. In the Nisan flashback scenes, however, he has midnight blue-colored hair. The hair color change is never explained in the game or in Perfect Works leading to a few theories to explain it with the most common one being that his hair changed color presumably as the result of Nanomachines prolonging his life.
    • Despite the game implying otherwise, some fans believe that Fei and Elly' past lives as the Contact and Antitype mean that they, like Miang, are reborn after they die every time instead of only being reborn a few times like the game seems to imply, and the only reason we see specific past lives is because they were the only ones who either were important, or met each other.
    • One way to interpret the Faux Symbolism issues later mentioned (the Hebrew named cities, the religious kitchen sink factor with both the Ethos and the Nisan Sect) is that the reason the planet's religions are extremely messy pastiches is as a part of the deep-time setting - in Real Life, religions and their practices/influence/mythology/etcetera have changed, sometimes dramatically, over far less than the game's 10,000+ years into the future. So it could be seen as Faux Symbolism and appropriation, or as how religion, mythology, and spirituality changed over 10,000+ years, space travel, and the settling of a planet via cataclysmic events.
  • Fan-Preferred Couple: Canonically Bart's love interest ins his fiancee and cousin Margie, and though the two seem to treat their arranged marriage as somewhat an obligation, they care a lot about each other and semi-official art depicts them as Happily Married. Possibly because of these Squicky elements though, it was and still is far more popular to pair him with Billy, whose Vitriolic Best Buds relationship is perceived by some to come off as Like an Old Married Couple, and which spawned a good deal of doujinshi in the 00's.
  • Faux Symbolism:
    • In a game that arguably handles many of its symbolical and mythological themes quite well at times, a lot of the towns are named after months in the Jewish calendar for no adequately explained reason.
    • Most jarringly, if ironically easy to miss, the Ethos is structured like and has symbols similar to those of Christianity, especially the Catholic Church, with confessionals, cross-like shapes, and bishops. In its theology, however, it is completely lacking a historical Messiah figure and due to that has more in common with Judaism or Islam, doctrinally speaking, than with Christianity, meaning all those crosses, habit-wearing nuns, cassock-wearing priests, and hierarchical/practical similarities to the world's largest Christian church are misplaced, sometimes severely. The most blatant of these loosely-Christian references is a scene with three crosses on a hill with a name very similar to "Golgotha", the Hebrew name for the hill where Jesus was crucified; but even the most Messiah-like figure in the game (from a Gnostic-type religion, not from Ethos) didn't die by Crucifixion or anything remotely like it.
    • Some of the character names are guilty of this as well. For example: Elly's squad early in the game is filled with characters named after famous psychologists, such as how Helmholz is named after Hermann von Helmholtz, a German physicist and physician, and yet Helmholz is nothing at all like the man, and is simply an antagonist. The Elements are all named after the different types of angels, such as Seraphita being linked to the name Seraph, but none of them have any actual ties to angels aside from their connections to Solaris.
  • Fetish Retardant:
    • All of the pixellated nudity— even if the character designs make you think you'd want to see it, it's really not exciting. At all.
    • The implied Chu-Chu orgy in Shevat qualifies too, though that one takes Fan Disservice to horrifying levels.
  • Game-Breaker:
    • For much of the first disc, Vierge + Ether Doubler + Power Magic = one shotting bosses with Aerods. Ether Doubler does exactly what it sounds like: doubles the power of any Ether attack, at the expense of also doubling the EP cost. What makes this combo truly broken is that Aerods don't have an EP cost; they're powered by Fuel. Thus, they get massively buffed by Ether Doubler for free. A bit later you get the Power Crisis which causes the user to deal more damage at lower HP - except it's a bit too effective, losing even a few HP makes the user the most powerful attacker in the game and at low HP you can kill a gear sized enemy on foot.
    • The Holy Pendant doubles the duration of in-battle effects on the equipped character. Possibly due to a programming oversight, this bonus also extends to Gear combat, which means that the equipped character can spend up to six turns in Hyper Mode. Miss your chance to buy one? Never fear! You get one for free when Billy joins you.
    • More generally: Citan is obscenely powerful, due to his high HP and the highest Agility stat in the game. The Power Crisis accessory is obscenely powerful, due to increasing the equipped character's attack power by huge margins as their HP gets lower. Equip Citan with Power Crisis, let him get hurt, and you have an unstoppable death machine on your hands. And just in case you don't think he's broken enough, later on he gets his sword. WordOfGod has stated that this wasn't actually intentional, as his massive speed was supposed to be in line with Bart's speed, meaning while he still would be amazing, he wouldn't be finishing his second turn by the time everyone else but Emeralda would be getting to their first turn.
    • Equipping Elly with three Power Magics and using Aerods (or ether) is less of a nuke than an Ether Doubler, but they aren't Permanently Missable and are the optimal alternative. Most bosses can be taken down after four or five hits with Aerods on Power Magics, at least while Elly's still in the party.
    • She may not quite be a Gamebreaker since you can only get her in a side quest before the final dungeon, but Adult Emeralda deserves a mention. She gets a hidden 20% bonus to both physical and Ether attacks, she's got the second best Agility after Citan, and all of her other stats will boost for every single level-up, including unusually good HP gains, so if you haven't been leveling up your characters much, she really has a lot to gain from her upgrade. She combines all of the best traits of Fei and Elly. Not a coincidence, given that their previous incarnations created her. And even though the final dungeon is Gear based, her high Ether stat does carry over into her Gear.
    • Bart's "Wild Smile" ability qualifies, due to the fact that in can affect most bosses. The effects also stack, so while one casting results in "enemy usually misses", two or three means "can't hit the broadside of a barn". He also already knows it as soon as he joins up and the game has a way of telling you that you'd better use it if you want to live by making the first boss after Bart joins nearly impossible to defeat without using it on him.
    • Rico. You can play him in a few ways. You can give him accessories to make him as fast as all the other characters, giving him preemptive attacks over enemies. Or you can boost his strength even further with accessories and he can clean up when his turn comes up last. Being the last to go, he can also use healing items or whatever's needed to prepare for the next round. Otherwise, Rico steamrolls over everything to end the fight.
  • Goddamned Boss: Bart's one on one fight with Ramsus' early in the game is an unusually hard fight for how early it is, but not because it is a super complex fight, but because you're fighting a decently strong foe alone, who is supported by Miang who can heal and remove any debuffs you use on Ramsus, negating Bart's Wild Smile from being a factor. Ramsus isn't necessarily hard on his own, since he cannot one-shot Bart, and even slightly under leveled, Bart can survive a few hits, but the fight is still hard for not really playing by the same rules that most boss fights do. Not helping is Margie's support, which on paper is supposed to balance it, but when Ramsus can hit for anywhere from 20 to 70 damage in one combo, and Margie often only heals 20 HP, it can snowball into a losing battle quickly. It doesn't help that the fight is one of the few to rely on paying attention to the bosses animations, as Ramsus has a counter stance that deals a lot of damage to Bart if you don't pay attention.
  • Good Bad Translation:
    • While the line about Yui beating Citan in a sword duel and falling in love with him while he's recovering is actually a mistranslation (according to Perfect Works, the one he raised his sword against was her grandfather Gaspar), it's widely considered an awesome story element and is well-enshrined in the fandom by now.
    • Krelian's name was supposed to be Karellen, an intended reference to Childhood's End. Due to a mistake, his name was instead translated as Krelian instead. Some players actually prefer this over Karellen though, as instead of being just the name taken straight from the book, instead it makes the name more unique, while still being able to be traced back to the source.
  • Hilarious in Hindsight:
  • Ho Yay:
    • Citan and Fei both bring the Ho Yay despite Citan's marriage to Yui and Fei's and Elly's Reincarnation Romance. There's dialogue referring to their sharing baths. They share a bed for a "light nap" in a scene full of Double Entendre. Citan reacts rather jealously to the thought of women and Fei at least twice. Also, Id outright says he "likes" Citan, with fully homoerotic implications. Also, outside of gameplay, Citan and Fei (even as Id) hold back in fighting each other, well before Fei's love for Elly gives him temporary control over Id.
    • Some of Hammer's comments make him come off as Ambiguously Camp Gay, such as his closeness with Rico, and a bit of flirting with Citan.
    • Ramsus's intense anger at the other Elements having abandoned him, as well as their intense admiration of him in the past, is implied to be due to more than just friendship or respect for a Visionary Villain. It's intensified by Word of Saint Paul via the short story manga Liquid Sky, written by the main writer, which strongly implies Ramsus and Sigurd to have once been an outright couple when they were in Jugend, and that part of Miang's emotional abuse of Ramsus involves cutting him off from Sigurd's attempts to reconcile.
    • Shortly before Miang hypnotizes Elly, she notes her beautiful eyes, leading to parts of fandom treating her as a Memetic Molester.
  • Inferred Holocaust: Almost everyone on the planet is dead by the end of the game due to either becoming part of Deus (who is blown up at the game's end) or getting killed during the many catastrophic events of the game. The handful of survivors only have one working Gear (even if it's incredibly powerful) left to protect them from the dragons and dinosaurs running around the planet, the group of people in charge of finding new technology are dead, and the technology needed to get off the planet may have been irrecoverably damaged, depending on what Deus did to the remains of the Eldridge. It isn't impossible that the remainder of humanity survives past the events of the game, but it'll certainly be an uphill battle for them.
  • Iron Woobie: You'd never know how much childhood trauma Bart went through if Margie didn't tell you.
  • Magnificent Bastard:
    • Grahf, the enigmatic Arch-Enemy of Fei, is a Wild Card with a hidden agenda. Actually one of Fei's past life Lacan, he was a former peace advocate but after his beloved Sophia, Elly's past life, sacrificed herself for his sake only to learn that the history of his world is actually being controlled by Miang and Deus in a cycle to resurrect Deus, Lacan decided it was better to destroy the world to free everyone especially Sophia, ascending as his own being from Fei becoming Grahf. Planning to help Miang and Deus before betraying and destroying them using the power of the Contract, Grahf first attempted to possess Fei, but ended up taking his father Khan instead. Regaining control from Khan years later, Grahf masterminded Fei's journey to power, arranging his village's destruction and empowering his enemies to possess him later when he is strong enough to defeat Miang and Deus. However, when Fei ended up defeating him in their final battle, Grahf realizes that Fei alone could defeat the two not him, and sacrifices himself to save him, using his final moments to beg Fei to save Elly.
    • Krelian, leader of Solaris, is a brilliant man with goals beyond the mortal world. Once the devout follower and friend of Lacan and Sophia, when Sophia died to end a war, Lacan lost his faith in the god Sophia believed in, further spiraling into depression after learning the truth of his world being manipulated by Miang and Deus since the beginning. With ambitions to ascend to godhood with the rest of civilization in his pursuit for peace through Deus, Krelian worked with the Gazel Ministry, Cain and even Miang herself, appealing to them by using his expertise in nanotech to lead their cruel experiments and operation for a dystopia, while secretly set-up their demise, deceiving Ramses into killing Cain, and using a virus to delete the Gazel Ministry. With his plans in motion, Krelian succeedes in ascending with plans to take the rest of humanity with him, only to change his mind upon seeing Fei and Elly's determination, using his powers to instead help them defeat Miang and Deus for good, and returning them home before going with the Wave of Existence to the land of god believing he does not belong back home after everything he has done.
  • Memetic Molester: While Miang's experiments as Karen are stated in the story to be for the purpose of finding the Contact, one can't help but wonder whether some of the probing she did to Fei as a child was really necessary... On top of that, she comments on how "handsome" Fei is when he participates in the martial arts tournament, knowing that he's that same child who grew up. And don't think the girls are safe from her, either. Miang saves Elly from Dominia's wrath, only to get alone in a room with the Gebler-officer-turned-traitor and... admire Elly's eyes before hypnotizing her. We know about Miang's "arrangement's" to sabotage the Yggdrasil's engines using Elly, but were those the only ones?
  • Memetic Mutation:
    • "Chu-Chu died for your sins!"Explanation 
    • "Master, Sir, did you just see my MAD SKILLZ?!"Explanation 
    • Grahf's runny nose.Explanation 
    • To a lesser extent, "This video has violated YouTube guidelines".Explanation 
    • "My Father? You mean my dad?"Explanation 
    • Various mishearings of the voice clip in the boss theme.Explanation 
    • The Exposition Chair.Explanation 
  • Most Wonderful Sound: The input of commands in battle.
    • The sound of EXP being added up at the end of battle.
    • Half of the game's in battle sound effects.
  • Narm:
    • The first time Grahf does his "Doth thou desire the power" speech after the fight with Vanderkam is treated very seriously, and the scene that follows is a big Wham Episode. However, the writers decided to have Vanderkam and Grahf's exchange almost completely revolve around saying power so often, that it becomes funny instead of tense. They say power nearly ten times, and each time they do, the scene becomes harder to take seriously.
    • The scene where Chu-Chu stands up to Achtzehn and inspires Maria to fight against her father in Shevat is supposed to be a dramatic and pivotal moment in Maria's arc, but a number of factors work against the seriousness and drama of the sequence that results in it becoming unintentionally hilarious. Stuff ranging from unfitting music, the sheer hilarity of Chu-Chu suddenly becoming big enough to fight a gear without build-up, and the overly drawn out scene of Maria running through all of Shevat to reach her Gear. These all make the scene hard to take seriously, and undercuts the moment in an accidentally comedic way.
    • The late game scene of all the heroes Gears being fixed to a cross to taunt Elly into coming out is supposed to be an intense and dramatic scene, but the fact the characters are just floating in front of the crosses, the sheer idea of nailing them to the crosses to begin with, and how some stuff looks off (such as Weltall's arms and Maria just standing on top of Seibzehn), make the scene unintentionally funny instead of tense. The fact Chu-Chu is also there makes it worse.
    • A scene in the ending wherein Elly trips, and Fei tries to go catch her. Fei shouts "EEEEELLLLLYYYYY!" while flat out diving to the ground like he's jumping off a diving board.
  • Nausea Fuel: The entire food processing plant. It's filled with victims of human experimentation, and you eventually find that the food and medicine of Solaris is derived from bloody piles of meat that turn out to come from Wels.
  • Older Than They Think: The game is often accused of homaging or even ripping off Neon Genesis Evangelion, which had only come out a year prior and shares a lot of superficial thematic similarities. However, most of the aspects of the game attributed to Evangelion are in fact homages to much older scifi works or explicitly came from concepts that preceded Evangelion. For example, many of Fei's personality traits attributed to Shinji are in fact a Shout-Out to Luke Skywalker, as the game is very open about its Star Wars inspirations, and Fei's troubled childhood and emotional instability were one of the earliest concepts devised for the game, back in 1994 when it was a prototype for Final Fantasy VII about a soldier with split personalitiesnote . Likewise, the heavy Judaeo-Christian and largely Jungian psychological themes are the result of shared Author Appeal from when the creators were still working on Final Fantasy VI; they're applied in a very different manner, being heavily allegorical in contrast to the more Freudian Evangelion, where the creator admitted to using them for Faux Symbolism purposes. Finally, the overarching Assimilation Plot is not inspired by Evangelion; rather, both were separately inspired by the same source, the much older Childhood's End, which was more obvious in the Japanese version where Krelian's name was a clear reference to Karellen from the book.
  • The Scrappy:
    • The cutesy mascot character, Chu-chu, is pretty widely reviled due to being obnoxious, vaguely creepy, nearly useless in battle, and incredibly at odds with the bleak, cynical tone of the game. While some of this can be attributed to being meant to be a light hearted character in a rather dark game causing some Mood Whiplash, Chu-Chu's lack of real character development, or really a need to be in the story made at all, makes them widely hated by many players.
    • Dan. Despite his minor role in the wider story, Dan is disliked for his design and unintentionally creepy personality (such as pushing Fei to get with his sister, including bringing up her breasts randomly). Whatever intentions were meant to exist for him largely were ignored because even though he rightfully is upset after Fei looses control at the start of the game and causes the death of his sister and a number of villagers, his bratty personality combined with his design really didn't do any favors for him.
  • Spiritual Successor: This game bears a lot of similarities to Neon Genesis Evangelion, many of which are likely coincidental due to the game's conceptualization preceding the latter, but which are so similar that it can feel like outright plagiarism. The story is filled to the brim with Humongous Mecha and symbolism linked to Judeo-Christian theology, the protagonist is a very psychologically-troubled teen forced to pilot a mech he wants nothing to do with, there's a massive Gambit Pileup between the Omniscient Council of Vagueness and the Big Bad who are both planning to invoke an Assimilation Plot on the human race for their own reasons, and both ultimately discuss the same dichotomy of what constitutes a more ideal existence for humanity: one without pain or individuality, or one rife with suffering but an opportunity for people to come together. Heck, both works also ran into production difficulties at the end, forcing the creators to get a bit...creative in how they wrapped their respective stories up.
  • Stoic Woobie: Rico, though he became more of a conventional Woobie when losing Hammer undid his stoic façade. Rico was still tough, but never quite as stoic after that.
  • That One Boss:
    • Redrum! Instant kills (that heal him!), area wide damage (that also heals him!), a ton of negative status ailments, and the highest HP of any boss fought up to this point by far.
    • Id in Zeboim certainly qualifies, especially if you haven't been leveling your characters enough. He attacks multiple times in one turn and is so strong he can kill most party members in one or two attacks. He also likes to dodge Deathblows, which few other enemies can do consistently.
    • Shakhan's fight is an annoying and hard fight, largely because he relies on switching phases. In his normal phase, he counters all attacks with hard hitting physical moves, or uses Seal, which not only hurts but can inflict Slow. In his second phase, he attaches himself to the Gate and recovers a lot of HP, but can't counter. The idea seems to be that the player carefully attacks during his normal phase, then when he switches to healing, unleash your strongest Deathblows on him, but he heals often enough that he can drag the fight out while slowly whittling your team down. Even if you have Gear equipment meant to reduce the damage of Seal, he does a lot of damage, and eats up a bunch of your Fuel.
    • Miang in the Opiomorph can be this due to it's Puzzle Boss nature. The boss has a gimmick that will possibly one shot and likely frustrate new players going in blind. This mechanic is that the boss will essentially "charge up" from the damage it takes, then counter attack with an ability that will do more damage depending on how much the boss takes. If you simply unload everything you have on the boss, it will very likely kill you instantly. But once you know this, the boss can go in the opposite direction of frustrating in that the boss can't actually hurt you unless you hurt it. So if you are extra cautious, the boss can take a rather long while to defeat. So the name of the game becomes doing as much damage as you can to the boss without going too far and getting yourself killed, which can be more frustrating than anything.
  • That One Level:
    • The Nortune D-Block Sewers are one of the longest, most annoying parts of the game. The level is a long maze, making it easy to get lost (despite the game giving you maps) and Redrum is That One Boss.
    • The Tower of Babel is an entirely vertical level made up of long jumping segments: if you fall, you end up back at the start. The platforming controls are abysmal and unresponsive, and the camera only has a few angles you can look at it from (and not every platform is aligned with these camera angles, making it extremely difficult to line up the jumps you can make). Another problem with this level is the high random encounter rate: in Xenogears, when a battle is triggered you can move around normally while it's being loaded, but you can't jump, so you may end up walking off the ends of platforms and falling accidently because of it.
    • The last dungeon of the first disc goes on longer than the Kislev Sewers and the Tower of Babel combined. To be fair, this is technically because it is two dungeons (Soylent System and Krelian's Lab) linked together. Making it even more annoying is that nearly every enemy has absurd Ether Defense. This hurts when Elly is one of your required characters. Krelian's lab is difficult not because of the length or encounters, but because since it's all very samey-looking hallways, it's extremely easy to be running in circles for over an hour.
    • Deus, The Very Definitely Final Dungeon. It's a huge, multi-level maze with an obscenely high random encounter rate, almost all of which are Seraphs. While the game gives you maps of the interior, they really aren't that useful, and they don't help with the switch puzzle on the lower levels. Did we mention there's a switch puzzle on the lower levels? Also, for one final kick in the teeth, at the end of the dungeon, you can visit Shopkeep Johnny, who has an option to teleport you out of the dungeon with no confirmation, meaning if you misclick, you will have to redo the entire dungeon.
  • They Wasted a Perfectly Good Character: Every playable cast member that is not Fei, Elly, Citan, or Bart have an interesting backstory and possible character arc that is never elaborated on. Rico is the secret prince of Kislev, Billy is the one remaining member of a religion that turned out to be evil, Chu-Chu is a member of the only other race of sentient beings on the planet which is going extinct, Maria controls a giant semi-sentient robot that may or may not be her mother, and Emeralda is the only sentient colony of nanomachines in existence. Emeralda does gets an expansion of her backstory in a side quest in late Disc 2 (she's the daughter of Fei and Elly in a past life), but it's easily missable if you don't have a guide. Rico at least has the justification of the second disk having planned to give him more to do but couldn't be done, but Billy, Chu-Chu, and Maria have practically nothing after their initial arcs are done, which stands out when Billy and Maria's arcs are fondly regarded.
  • Unintentionally Unsympathetic: Krelian was clearly supposed to be seen in a sympathetic light at the end, and both Fei and Elly are shown to forgive him for his sins, going so far as to beseech him to return so he can atone. However, the fact that he had turned traitor to join Solaris, ruled the world from the shadows for 500 years, conducted all manner of gruesome experiments on people during that time, was willing to commit genocide on the entire human race, wiped out 90% of the population, and frequently mocked those he wronged, all because he lost the woman he loved, does not afford him much love from many fans.
  • Values Dissonance:
    • In regards to Fei, a number of westerns see Fei as annoying or an idiot due to his habit of Parrot Exposition that makes him look like he isn't paying attention or is dumb. This is due to a combination of Realistic Diction Is Unrealistic, and the language barrier between Japan and the west. Both Japanese and English include the concept of backchanneling, interjections made during a conversation to show that someone is actively paying attention and engaging with the topic. In English, these are usually very short statements ("Uh-huh" or "Oh really?") and aren't often used in fiction, but in Japan, where it's called "Aizuchi", it can include repeating what is said as a question, or making comments about the subject, which is supposed to show the talker that the person listening is actively focused and reassures the speaker they're making sense. Since longer repetitions like that that would seem either rude (like you're interrupting someone's speech) or unnecessary in English, it makes Fei read differently to a western viewer compared to a Japanese player. He's meant to be seen as generally polite and always listening, even if he doesn't agree with the speaker, but to a western viewer, he comes across as not paying attention, or an idiot, when in truth it isn't that. For example: When Grahf taunts Fei about his father early in the game, Fei's reply where he seems to restate that Grahf was talking about his father makes sense to someone who is part of Japanese culture, but to a western player, Fei looks like he's an idiot for doing so (the translation also contributes).
    • To many Western players, Citan comes off as an untrustworthy, self-interested jerk at best. This is almost exclusively due to said Western players not understanding the samurai tropes that define his character and that his character development is the path from obligated samurai to free ronin, and also sometimes from Western players with a more standard Western understanding of Christianity not understanding his particular type of Gnostic Lucifer symbolism. Citan is mysterious for sure, but he's meant to be seen as consistently a force of good and on the side of the heroes, which to a western player, can come across as him being a Designated Hero instead.
  • What Do You Mean, It's Not for Kids?:
    • Just because the game has humongous mechas doesn't mean it's for kids. The protagonist having an evil Split Personality who is an omnicidal maniac who can and does commit genocides by himself, when one of the dominant religion is a front for a decadent dictatorship where being racist is considered to be a civic duty.
    • Not to mention God, Deus (well, not quite God, the Demiurge) is completely evil and to resurrect himself, 90% of the entire human race mutate into Wels, mini-Eldritch Abominations that become spare parts for him. And then there's the religious undertones, sporadic sexual content, and the overall general dark tone of the story. To put it in perspective, it is probably Square's darkest PS1 game, bar none.
  • The Woobie: Fei, with a side dose of Paranoia Fuel and Nightmare Fuel. He's unaware of his alters up until the fall of Solaris, and misses time - but he sees the missed time as being asleep/dreaming or a blackout. He literally doesn't know until that point that that's not actually sleep or a blackout - but his alter manifesting and lots of murder about to go down. His final fusion leaves him aware and with all of the memories of Id as well as of his reincarnations and his other alter.

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