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  • Alternative Character Interpretation: Hinted at by Word of God. Big Bad Wilhelm's plot involves resetting time over and over again to avoid the universe's eventual destruction. The characters argue that endlessly repeating the same thing simply for the sake of existence is meaningless, and put a stop to it. At this point Wilhelm may seem like a Well-Intentioned Extremist at best and pure evil at worst (he's directly or indirectly responsible for everything that happens in the series, including each character's individual traumas), but the post-game database suggests that the party's rejection of his plan was actually what he wanted, and that by continually resetting the universe he was actually "training" the collective consciousness of humanity to move on and find a way to avoid the universe's destruction, putting him in a much more positive light.
  • Base-Breaking Character:
    • Shion. For her detractors, she's obnoxious, selfish and overall unlikable. For her defenders, she's a compelling female protagonist (in a genre where those are extremely rare to boot) who manages to stay strong despite suffering massively from Deus Angst Machina and has an engaging Character Development, which makes her very sympathetic. The division was so bad that Tetsuya Takahashi, while creating Xenoblade Chronicles 1, went out of his way to make sure that the main character remained likable the whole way through.
      • The main point of this contention would be Episode III, particularly during the last third of that episode's story. While in the previous two episodes she had some detractors, the reception of her tended to be clearly more positive than negative. However, her fixation on going back to Kevin, utterly rejecting her friends and their attempts for help in the process to the point she even ends up turning against them made her extremely divisive. Not only in Episode III specifically, but in the series as a whole. Depending on your perspective, you'll feel sorry that her judgment has been derailed so badly, with some arguing that it's actually a very realistic depiction of a victim of emotional abuse that showcases the depth behind Shion's character, or your sympathy for her will just go out the window due to it not necessarily receiving a lot of onscreen buildup beforehand (although the Japan-only Episode I+II port does expand on this backstory a bit more). Although Shion eventually snaps out of it, for many, if not the majority of her detractors, it only happens when it's too little, too late.
    • Somewhat related to the previous one, we have Kevin Winnicott, also in Episode III. Depending on who you ask, he's either a compelling antagonist and a somewhat accurate depiction of an abusive romantic partner, or a disgusting Scrappy villain who, instead of waiting for him to get his comeuppance, you just wish he wasn't part of the story at all, since he brings everything down with him. A big reason for this is that although the story and even eventually Shion recognize that he was just being manipulative, the narrative still tries to convey that, at the end of the day, Kevin truly cared for Shion, even if he was misguided in trying to save Shion while still trying to follow Wilhelm's plan at the same time. At the very end, Shion has a heartfelt good-bye with him, stating that she understands why he went along with it, and decides to at least cherish the good memories. Again, there are people who thinks this development was compelling, while others don't buy it for one second.
  • Breather Level:
    • The Dammerung in Episode II. Shion is the only playable character so the enemies are scaled down in strength for her to handle solo, and all of them are weak to her default elements. There are also relatively fewer enemies overall and more emphasis on puzzles.
    • Chapter 5 in episode III has no combat at all, just exposition and exploration of Miltia and the Acute Neurosis Treatment Facility. You can't even get into combat if you try, since the party is restricted to only Shion and Allen, and you are blocked from using the Encephalon or entering previous areas with enemies.
  • Captain Obvious Reveal: Happens to Kevin twice, (see The Un-Twist below). Not only is it very obvious that Kevin is the Red Testament before the actual reveal, but when the characters travel back in time to Old Militia, they encounter a younger Kevin who is working as Professor Mizrahi's assistant. Even though its beyond obvious that it's Kevin, the game simply refers to him as "young man" for his first appearances and treats the reveal of his name as if it were a twist; Shion and Allen are also unable to figure out his identity until Mizrahi uses his name, though they do Handwave it by pointing out that young Kevin's personality is completely different than the Kevin they remember.
  • Common Knowledge:
    • So Xenosaga stopped at 3 episodes because Namco interfered after the 1st episode came out on account of it being a failure, right? Well not quite. Despite being a commonly accepted view and stated as fact, in truth Namco were very supportive of the team and helped with the development of the first game as much as they could, and while the first episode wasn't a smash-hit, it wasn't a commercial failure, selling generally pretty well in both the East and West. The decision to pare the story down to only three episodes covering Shion's time period was a voluntary choice that was made once it became clear the first game could only able to cover a small fraction of the storyline originally envisioned for Perfect Works Episode I. As for the second game, the team was changed up with the blessing of Takahashi himself, who was wanting newer staff to step-up and have the chance to show what they could do, but his frustrations with the development of the first episode and factors with the new team caused him to basically walk off the project for the second game before returning to the third in an advisorial role, with a team that was a bit all over the place. So while yes, the game had a rough development, it wasn't because of proactive meddling from Namco or bad sales, but a combination of internal problems and inconsistent material support for later episodes from Namco, whose CEO at the time favored a Tough Love philosophy towards Monolith Soft.
    • Xenogears, Xenosaga and Xenoblade Chronicles are NOT the same franchise. They are three separate IPs, owned by three separate companies, with three separate narratives and continuities, not meant to be directly sharing any form of universe, or even multiverse. While it's true that they share many elements out of the fact that they were created by the same group of people, for reasons that partially have to do with copyright, the connections are supposed to be only spiritual and conceptual, and nothing more (a bit like the System Shock and BioShock franchises, for instance). This is not helped by the fact that fans of Monolith's work like to lump them together anyway, even those who are 100% aware of this fact. Thus, they are called "the Xeno series" for the sake of brevity, which can be misleading for casual observers and newcomers (some fans have suggested to use "the Xeno games" or "the Xeno metaseries" instead, but with little avail). The ending of Xenoblade Chronicles 3: Future Redeemed finally does tie the whole meta series together, with some potent Wham Shots and Wham Lines at the very end, implying that a certain event that happened in Xenoblade was the catalyst for the disappearance of Lost Jerusalem in both Xenogears and Xenosaga.
  • Complacent Gaming Syndrome: Ziggy's pretty much never used outside of segments he's mandatory in for the fact that he's slow.
  • Complete Monster:
    • Episodes I & II: Patriarch Sergius XVII presents himself as the beloved spiritual leader of the galaxy, but in truth is the mastermind behind the U-TIC terrorist organization who seeks to conquer humanity. Once the owner of the original Zohar supercomputer, Sergius boosted its power by wiring it up to two innocent little Realian girls, keeping them in agony for over a decade while having them and the Zohar experimented on. When the Zohar was lost in the destruction of Old Miltia, Sergius began a crusade to get it back using U-TIC, and once he succeeds, he activates the Omega System to force all of galactic civilization to submit to him under penalty of death.
    • Episodes II & III: Dr. Dmitri Yuriev is the appallingly selfish "father" to major protagonist Junior, major antagonist Albedo, and over 600 other cloned "children". The first human to make contact with the Sentient Cosmic Force U-DO, Yuriev lives for centuries afterward, driven by fear of the entity and a desire to destroy it. Creating his clone "family", Yuriev sends them off to die in scores in the war against U-TIC, and periodically steals their bodies to cheat death. Resurrecting himself through his final creation Gaignun Kukai, Yuriev massacres all of Gaignun's staff when they get in his way, and retrieves the Zohar and the Omega System after Sergius' death to attempt to make himself into a god powerful enough to slay U-DO.
  • Contested Sequel: Being a Spiritual Successor, this is how many see Xenosaga as a whole in regards to Xenogears. Many people consider it a far less successful attempt in the type of narrative that Xenogears pulled off back in 1998. See Fandom Rivalry below.
  • Creepy Awesome: Albedo. Considered the most terrifying antagonist, not only in Xenosaga, but in all three Xeno franchises. Because of that, he's also considered the most compelling.
  • Draco in Leather Pants: Albedo is an unquestionably horrifying, sadistic, Ax-Crazy pedophile who enjoys terrorizing and murdering small robot girls - but he has white hair, so he's probably just misunderstood. May also count as Laughably Evil; he takes Ax-Crazy and sadomasochism to new heights but god, he does it with such hamminess.
  • Ensemble Dark Horse:
    • Although Andrew Cherenkov only appears in the first third of Episode I, he's one of the most beloved and memorable secondary characters in the franchise due to his tragic backstory and sheer Woobie factor.
    • Orgulla, boss from Episode II that is never heard from again after the fight with her, is nevertheless a very memorable encounter due to her being a schizophrenic fundamentalist cyborg.
  • Estrogen Brigade: As discussed by various creators for the game such as KOS-MOS' designer Choco, the series attracted a strong female fanbase due to the character-focused writing and discussions of issues that many women found relatable, such as abusive relationships, misogyny in the workplace, and recovering from trauma.
  • Fandom Rivalry: To an extent, with both its spiritual predecessor Xenogears and its Spiritual Successor Xenoblade Chronicles.
    • Xenogears: The contention is about which of the two had the best narrative. Both go for huge space opera epics, with a millennia-extending and mystery-ridden Jigsaw Puzzle Plot that demands the player's full attention to understand what's going on. While it's mostly accepted that Xenosaga was more consistent in its presentation and gameplaynote , Xenogears is generally considered to have pulled off a more satisfying and intriguing story overall regardless. Something a bit less clear cut is which of the two games have the best characters. Xenogears tends to be favored when it comes to the plot and worldbuilding and the protagonistsnote , while Xenosaga is considered to have stronger and more unique Character Development arcs and be better at making the entire cast more or less relevant the whole way throughnote .
    • Xenoblade Chronicles: In this case, usually over the Story to Gameplay Ratio. Xenosaga fans typically regard Xenoblade as having dumbed down story, characters, and themes to appeal to Lowest Common Denominator audiences, whereas Xenoblade fans argue that Xenosaga was too ambitious for its own good and required too much outside reading to make enjoyable, whereas the Xenoblade franchise managed to deliver stories that were largely told onscreen without heavy reliance on All There in the Manual. At the least, Xenoblade tends to be viewed as beating the other franchises out of the water in the gameplay area due to its more modern Wide-Open Sandbox design and less reliance on overtly-long cut scenes (which creator Tetsuya Takahashi said was deliberate, describing the cutscene-heavy approach of Xenosaga as a developmental dead-end).
  • Faux Symbolism: The series is dense with namedrops to philosophy and religion, but it's difficult to tell how much of the symbolism and references are really symbolic and how many are gratuitous, not helped by the aborted and rewritten plot. In general, Xenosaga is considered much worse about it than the Shown Their Work Xenogears, where most of the religious and philosophical terms had direct thematic or allegorical applications, or than Xenoblade Chronicles, although that's because there's less of it there.
  • Fridge Brilliance:
    • Jr.'s best weapon in I was the Blood M9, which becomes his first weapon in III because there is no equipment changing in II.
    • At the beginning of Episode I, it's mentioned how Virgil has a condition stemming from the consumption of Realian Tissue. At the time, you're told this is treated like a kind of drug to some people, and Shion is horrified at the implications. Later, you discover that the Realian Febronia donated some of her organs to him to save his life, and then suddenly everything clicks into place.
    • When Jin and Margulis have their fights in Episode II, they're notably rather down-to-earth despite their Charles Atlas Superpower capabilities, and while there are some flashy movements, all of it is fairly realistically choreographed and relatively practical. But they're also both somewhat stumbling about for parts of the fights, Jin's injury in the first not withstanding, and clearly not as good as the story touts them to be. Then you look at the flashbacks and realize the two of them, for as badass as they are, got old; Jin himself remarks that becoming a bookstore keeper hasn't done him much good for his skills. They're so extraordinarily powerful that any individual attacks would paste most other combatants, but are ultimately mundane and rusty by their own standards.
  • Game-Breaker:
    • Every iteration of Erde Kaiser. In the first game it's guaranteed to do 9999 damage, meaning the only enemy in the game it can't one-shot is the final boss, which has about 16,000 HP. The second game remedies this by making it so that you can't actually get it till post-game.
    • Xenosaga I had the Bravesoul and Golden Dice items which both increased attack power as the equipper's HP got lower, letting the player get a maximum of about 200% damage. The drawback of dying in one hit could be controlled with Safety Limit, which guarantees survival with 1 HP once per cast. Jr. in particular makes a joke out of every boss in the game partly due to his exclusive Dandyism, which stacks with Safety Limit and has a similar effect, but also due to the items only working with physical attacks, which he packs more of than any other character in the game.
    • The Casino from which you purchase the aforementioned items also includes a healing item pack (consisting of a Med Kit, an Ether Pack, a Revive! and a Cure-All) for a paltry 100 coins. By playing Poker it is trivially easy to get several thousand coins for the work of minutes, insuring you'll never have to spend a single red cent on healing items ever again
    • Not as extreme, but for whatever reason, MOMO is ridiculously powerful in Xenosaga II. In the first dungeon, Jr, chaos, and Ziggy do around 50-100 damage. MOMO does close to 200 and never lets up as the game progresses. She can learn a skill that doubles Ether damage. For any other character useful, but for MOMO, incredible because her basic attack is Ether based.
    • Xenosaga III's ES battles became exponentially easier once you got your hands on the Level II Anima Awakenings, which hit most if not all mooks on the screen for ridiculous damage. You could simply charge these by walking into a battle and retreating over and over again, then firing off your BFG (or BFS) once full. Also a great way to grind for money and skill points later on.
    • Xenosaga III also brought you Blood Dancer, which let KOS-MOS and MOMO turn red. Then take down the final incarnation of aforementioned Erde Kaiser, itself a game breaker, singlehandedly. The reward, Erde Kaiser Sigma, who, when summoned by someone under the influence of MOMO's Magic-Attack buff, can One-Hit Kill the FINAL BOSS.
    • Xenosaga III tends to be filled with these. Jr. and Shion can essentially become invincible for a couple of turns via Phantom Fly, a Master Skill that allows them to evade essentially every attack in the game. While it is normally tempered by an absurdly high EP cost, there's an accessory that you can get with a relatively easy sidequest near the end of the game that reduces SP cost to 1. Add the two together, and you get either Jr. who can support with the best of them, or Shion, who can inflict reasonable damage, break, and heal. And are invincible.
  • Genius Bonus: There's a few of them littered throughout the trilogy, the most obvious being that Sellers is a not-so-subtle Captain Ersatz of Dr. Strangelove, who was played by Peter Sellers.
  • Hilarious in Hindsight: Jr. remarks how T-elos bears a striking resemblance to KOS-MOS, one can wonder how he'll react if he ever meets Elma.
  • Ho Yay:
    • Shion and KOS-MOS's ambiguous friends or mother-daughter relationship ends up coming off more romantically charged at times. It's especially prominent in Episode III where we hear that KOS-MOS's awakening required her and Shion to grow close.
    • Albedo's brother complex towards Jr. retains the same sexual stalkerish undertones as his interest in MOMO, to the point of remarking on his sweet scent and getting a bit excited when he impales him.
    • It's known that Jin and Margulis used to be friends, and in Episode III you can find Jin's bathing suit in Margulis's room, for some reason. Margulis also describes his enthusiasm for fighting Jin in terms that verge on sexual.
  • Improved Second Attempt: After Episodes I and II were both criticized for having art styles that suffered from Unintentional Uncanny Valley, III went for a hybridized style that was widely praised for being eye-pleasing and avoiding the pitfalls of both.
  • It Was His Sled: Jesus Christ physically appears in Episode III as a plot-crucial character, along with the Apostles and Mary Magdalene. The previous games hint at chaos (whose true name is Yeshua) being Jesus or having some kind of connection to him, although exactly what is kept a mystery until the third game, which reveals that chaos was not Jesus himself, but a God in Human Form who was Jesus' close friend and inspired by his message to function as Jesus's divine half and perform the miracles typically accredited to him, in the game's particular spin on Gnostic theology. Many were so caught off-guard by the Shocking Moment of a JRPG having Jesus show up directly in a Space Opera that it's one of the few things casual audiences know about the game.
  • Jerkass Woobie: Vergil. While Episode I showed him to be a racist bastard who hated Relians for seemingly no reason, Episode III revealed that it wasn't for no reason, driving him to became the cynic he is during the present.
  • Low-Tier Letdown: Ziggy can hit quite hard and withstand a lot, but because he's slow most people would rather just use MOMO, chaos, or Junior instead.
  • Magnificent Bastard:
    • Doctor Sellers is the epitome of cold, amoral scientific genius. A disciple of the famed Professor Joachim Mizrahi, Sellers betrays his mentor to the U-TIC terrorist organization, then later sees to it that the now-deceased professor is framed for the destruction of Planet Miltia, turning him into the galaxy's boogeyman overnight. In his efforts to prove himself Mizrahi's scientific superior, Sellers offers his genius to multiple factions, from U-TIC to their foes in the government, constructing wonders such as the space station Merkabah and a working replica of the Zohar supercomputer. When finally confronted by the main characters, Sellers decides to simply leave, having no stakes in the conspiracy surrounding the Zohar whatsoever beyond demonstrating his own brilliance, which he has already accomplished.
    • Wilhelm is the ultimate puppetmaster behind every conflict in the world of Xenosaga. Ostensibly the CEO of the MegaCorp Vector Research and Development, Wilhelm is in reality an ancient being tasked with preserving the existence of the universe by any means necessary, regardless of the consequences to individual lives. Deciding that the best way to preserve the universe is to Restart the World repeatedly using the ancient Zarathustra Mechanism, Wilhelm manipulates both sides of the war between the Galactic Federation and U-TIC, using his money and his agents, the Testaments, to guide events to the point where the items and people he needs to activate Zarathustra will be brought directly to the device. His actions engineer conflicts that annihilate entire planets, but as far as Wilhelm is concerned it's all for the best to ensure the universe's safety, and even when the heroes successfully turn the tables on him, mortally wounding him and wrecking Zarathustra, Wilhelm simply reacts with bemusement at their choice of an uncertain future before vanishing with a smile.
    • Joachim Mizarhi, father of Realians, is one of the universe's secret heroes. Lead researcher of the Zohar, Joachim intended to use its secret to save his child, but later formed U-TIC to counter Yuriev and the Federation's after destroying his planet. Learning the Zohar's secrets, he made the Lemegeton, intending to use it to resurrect Sakura, but realizing the danger amends his sins. Overloading the Song of Nephilim after U-TIC decided to activate the Zohar, he intends to banish First Miltia, the Zohar, and Gnosis, before putting the Y-Data in MOMO leaving key data to stop the future disaster after his death, making himself look mad to hide his true plans, watching at the Beach of Nothing to see his plan come to fruition.
  • Memetic Molester: Albedo is a little too fond with MOMO and Jr.
  • Memetic Mutation:
    • You will not be able to hang around Xenosaga forums or watch Xenosaga videos for very long without hearing "SHION. MY APPEARANCE IS DOWN 5%. I NEED TO BE CLEANED." You just won't. She keeps the line as a joke in all of her crossover appearances.
      • Namco Bandai even hopped on the bandwagon with Tales of the Abyss. There is a doll that Anise can get (the Artificial Life Form) that gives Tokunaga KOS-MOS's visor, the X-BUSTER arte/attack, and the end battle quote of "Enemy appearance down 5%. They are nothing."
    • Helmer's "UUUUUUUUUUUU-DOOOOOOOOOOOOOOOO" line from Episode I has gotten a lot of this, particularly in LPs.
    • Certain versions of Episode II released alongside a special-edition toy figure of KOS-MOS that proved to be so poorly made that it was promptly dubbed Jashin ("Evil God") MOK-KOS.
    • A good chunk of Albedo's dialog, with Ma Belle Peche being the most notable.
    • Jr. yelling "YOU DAMN BITCH!" at Orgulla became pretty popular due to how forced it sounded.
    • The fact that Jesus Christ appears as a plot-important character in a flashback, complete with in-game model, has led to its fair share of memes treating Jesus as a character who originated from the Xenosaga franchise.
  • Misblamed:
    • Namco meddling is often blamed for the troubled development of the series. However, in truth, it was a combination of technical issues and several decisions from Takahashi himself due to suddenly shaking up the development team for the second game which resulted in a lot of its issues.
    • A lot of the notoriously long cutscenes gets blamed on the creators abusing Auteur License and getting carried away with the story they wanted to tell, especially since Xenogears was also known for its lengthy cutscenes. However, the developers revealed that the long cutscenes are actually Padding used to get around the fact that the game had quite a Troubled Production in which they had difficulty getting the gameplay engine to work correctly until a year before the game released.
  • Moe: MOMO seems to have been designed specifically to be as Moe as possible, what with her pink hair, childlike appearance, sweet personality, and the fact that the game likes to make her suffer.
  • Moral Event Horizon:
    • While it has been trampled to bits by the many villains of the series, the most obvious and earliest example takes place for the character Virgil. When you meet him in the first game, he hates Realians with a passion and has even eaten their flesh in the past. He crosses the Horizon when he decides, in order to protect himself from an oncoming swarm of Gnosis, to input the Override code into some nearby Realians and then self destructs them.
    • Yuriev crosses it when he uses his appearance as Gaignun to get close to Mary - and shoot her in the gut.
      • He just gets worse, ordering Nigredo to kill all the URTVs who survived the upcoming Miltian conflict, especially URTV 666 (Rubedo, aka Jr.) because his Red Dragon mode posed a threat to Dmitri. Plus him planning to send all the URTVs except Nigredo into the conflict in the first place knowing that it was extremely likely to cause a reaction that would incinerate the surface of the planet (killing all of his URTV children as well as every living thing on the planet) and was callously planning to use that to further his own political position. His reaction to being questioned that it was worth it to destroy Miltia if it got rid of U-DO? Yes.
      • Furthermore, he orders the murder of every man, woman, child, and realian on the Durandel save the four people who were useful to him.
    • Voyager crosses it when he murders Ziggy's/Jan's wife and adopted son.
    • Albedo crosses it when he mind rapes MOMO.
    • Wilhelm manages to cross it more time than the rest of the antagonists combined during the last act of Episode III.
  • Older Than They Think: The reveal in Episode III that KOS-MOS's true identity is Mary Magdalene, who was found in Rennes-le-Château, the site of many Mary Magdalene-related conspiracy theories came soon after the release of The Da Vinci Code, which took the world by storm at the time and woke up a lot of popular interest in the subject due to said character being at the center of its plot and the story being based off of one of the conspiracy theories associated with said site. However KOS-MOS was always intended to be Mary Magdalene since Episode I, before The Da Vinci Code was released, instead being based more off of The Holy Blood and the Holy Grail, the book that inspired it.
  • Once Original, Now Common: All three episodes were considered quite high tier in regards of graphical prowess when they first came out. However, nowadays Episodes I and II in particular are considered considerably dated. To be more specific:
    • Episode I is the one hit the hardest by this out of the trilogy. The graphics were actually quite impressive back in 2002, specially during the most epic cutscenes. The space battles were particularly noteworthy. However, the characters look quite stiff and lifeless by today's standards, and they tend to fail to live up to the emotions the game is going for for modern audiences. The anime style character designs are ironically partially to blame too. Although the character models were pretty impressive when they first came out, probably the most successful execution of that particular style up to that point (they were missed in Episode II for a reason), the primitive facial animations make them look too dead-eyed and doll-like now, and the exaggerated facial features only draw more attention to it.
    • Episode II is the most ironic case, since the change in character design for a more realistic approach, while heavily criticized when it first came out, has made the game to arguably age more gracefully. Of course, the far improved animations, specially in high-quality cut scenes, is a big responsible for this. But even in low-quality cut scenes, the more proportionate face features makes the lack of facial expressions to be far less jarring than in its predecessor. However, the lower polygon count of character models in said low-quality cut scenes look still quite dated on their own, and the fact that you have the far more successful high-quality models to compare them to makes them more noticeable. Not to mention that the animation tone problems still apply.
    • Episode III is the one entry that manages to escape almost completely. The high-quality cut scenes are quite a view even today, thanks to the experience that Monolithsoft had gotten with the previous entries, managing to actually execute the anime style more successfully without the lifelessness of Episode I nor the mismatch of Episode II. The decision to do without low-quality cut scenes in the style of the previous two entries, opting for using old-school text boxes (albeit voiced) instead, also proved to be a wise solution, long-term. They may look less cinematic, but since the camera is almost always pulled back, they also manage to hide their shortcomings far more successfully. Many people argue that Episode III just needs an HD upscale to be considered at least decent for modern audiences.
    • Related, but the soundtrack, despite that it's one of the best aged parts of the trilogy. A modern player looking back at the series might wonder why the first game advertised that it used the London Philharmonic Orchestra for its soundtrack. Many people might not think about this since video games have joined film in keeping the orchestra alive, but in the Turn of the Millennium, this was quite unusual to see in a video game.
  • One-Scene Wonder:
    • Orgulla is given a lot of characterization for the one boss fight you have with her and the cutscene before and after said fight, only to never be seen ever again to the point of being completely removed from the Xenosaga I&II Polished Port. It's probably what made her such an Ensemble Dark Horse.
    • Although Patriarch Sergius XVII is the one of the primary antagonists of Episode II, he's a blip on the radar in the series as a whole.
  • Only the Creator Does It Right: Some wanted to see the compressed adaptation of Episodes I&II on the DS simply because this one had more involvement from Takahashi. Many criticisms of episode II can be summed up as this.
  • Padding: Episode II is nearly padding incarnate; the actual main story line is very short, but most of the main dungeons are very long and full of backtracking, and the on foot battles can drag forever due to the stock and break system. The Ormus fortress dungeon is arguably complete filler. And the game is also chock full of lengthy fetch quests.
  • Presumed Flop: A lot of people have the perception that Episode I, despite the majorly positive reception from critics and fans, was a commercial flop, which was what prompted the changes in the series moving forward, specially shortening the original 6-part story to a trilogy. However, this wasn't the case. The game was one of Namco's biggest sellers of 2002, managing to even outsell a heavy hitter like Tekken 4, and the series gathered enough good will for Namco to green light multiple spin-off games and even an anime adaptation. The disappointment wasn't so much about finances as much as management. By Takahashi's own admission, the game's Troubled Production was more due to the lack of experience of the team and his own shortcomings as a director when it came to project management, which were an almost beat-for-beat repetition of what happened with Xenogears. The result was that the team only managed to tell a mere 20% of the first story arc. As in, the story that was supposed to span the first two episodes of the entire saga. Meaning that completing the entire 6 part epic Takahashi envisioned would have needed, not 6, but a whopping 15 game series spanning until, at least, the 2030s. Xenosaga would have needed to become a world-wide pop culture Juggernaut of the level of Star Wars itself in order to at least ponder such a proposition. The perception is true when it comes to Episode II, though.
  • Platonic Writing, Romantic Reading: The developers seemed to intend for KOS-MOS and Shion's relationship to appear platonic, initially starting off as almost a maternal relationship on Shion's side, but they typically appear MUCH closer than that. For what it's worth, the writers seem to flipflop between portraying their relationship as romantic or a mother-daughter one. Or possibly both, considering the motherly traits of various other official Xeno love interests.
  • Polished Port: Despite the technical downgrades necessary to make it run on the Nintendo DS, the various changes Xenosaga I&II makes to the story and gameplay are generally considered to make for a vastly improved experience in many ways, especially for the heavily-maligned Episode II. The plot of both games was heavily rewritten to be more cohesive and less confusing like the single game they were originally intended to be, and the static anime cutscenes avoid the Unintentional Uncanny Valley issues that plagued its console equivalents. Sadly, it was never brought to the West.
  • Robo Ship: Shion X KOS-MOS, or any ship involving KOS-MOS.
  • Scrappy Mechanic: The Stock system in Episode II, which slowed down the pace of the battles to a turtle's crawl.
  • Shocking Moments: Off the charts in the scene where Shion finds out that she made contact with the Zohar and summoned the Gnosis, leading to her Heroic BSoD.
  • Stoic Woobie: Jin truly has a sucktacular life, on par with Shion's but keeps it all to himself. Implied to be because he doesn't want to 'burden' Shion with his own problems, as he feels partly responsible for not being able to help Shion with hers.
  • Surprisingly Improved Sequel: Episode 3 goes out of its way to reverse nearly everything that was disliked about the second game; the battles are faster paced with a more streamlined break system and no more field effect roulette, characters once again learn abilities by leveling and no longer have identical skill trees, character equipment is back, and stores return. It also does a lot to improve on issues people had with the first game, such as the weird artstyle and E.S. combat being significantly improved from that of A.G.W.S. combat.
  • Sophomore Slump:
    • Episode II is considered the worst of the trilogy, if not downright a Franchise Killer. On its own, it isn't necessarily outright bad, with some saying it's generally solid, but as the middle game that clashes with the first and third game, it suffers from that middle spot due to the design choices. Many people gave up on the series altogether with that game for multiple reasons.
    • Some would consider Xenosaga itself to be this, smack in between Xenogears and Xenoblade. Due to the Troubled Production and massive writing shakeups plus the sequestering of important story content to unobtainable spinoff media, the game is often considered worse than Xenogears, which at the very least told a generally complete story despite similarly rough development, and Xenoblade, which was made with as smooth of a development as could be done, and released to great success. While Xenosaga has fans, it lacks the strengths of either title, on top of being the hardest to actually find a copy of.
  • Superlative Dubbing: While it has shown its age (and in many ways has some bizarre Lip Lock made even worse in the first game), this was considered to be a pretty solid dub. Many people preferred the english voices for the amount of Large Ham and even Epcar's Dull Surprise performance of Ziggy (especially in the first episode) even made sense. Special mention to Crispin Freeman as Albedo, who's terrifying portrayal as Albedo made him easily one of the most engaging characters in all of Monolith Soft repertoir, and possibly their best villain up to this point. The English voice of KOS-MOS is also another special mention, due to how Bridget Hoffman managing to deliver impressive robotic monotone voice fitting for an android like her and juggling with her more humane lines in Episode 3.
  • That One Boss: The Black Testament in episode 3, for more reasons than one. The battle itself is very tough; the testament hits like a truck and also has an annoying area of effect attack that causes poison, and can temporarily make himself immune to break damage and physical damage. But the circumstances around the boss are also a pain; earlier in the chapter the characters suggest Shion play a game of Hakox to relax, but it doesn't warn you at all that starting the minigame is a point of no return. As soon as you leave Hakox, a series of cutscenes begin that lead straight to the boss fight, with no chance to re-equip your party or even save. Lose to the black testament and you also lose all the progress you made in Hakox before the fight.
  • That One Level:
    • In Episode 1, the Song of Nephilim. A very long dungeon with different gimmicks and enemies in each of its three towers and only one save point. The enemies are probably THE strongest regular enemies in the entire game, with nearly all of them having hard hitting area of effect attacks, huge HP, and often come in groups of three or four. Also features four bosses, all of them fairly tricky. The final dungeon that follows is actually a bit of a Breather Level in comparison.
    • Episode 2 has the Ormus Stronghold. Your descent isn't particularly bad, if not a bit annoying for some hard-hitting enemies who can out-prioritize your own boosts and use an attack that's almost guaranteed to kill a party member. After you initiate the self-destruct sequence, you're given half an hour to ascend back to your E.S. crafts. Conceptually this doesn't seem so bad, but in execution it's absolutely hellish, even if you opened that shortcut earlier. The timer does not stop for anything but pausing and menus, meaning the clock is ticking for every battle (that you can't run away from, btw) you need to fight on your way back up. The enemies are just as challenging/obnoxious. Good luck!
    • In Episode 3 it's the Merkaba, not because it is really that difficult (it does not even have a boss fight) but because it is full of backtracking. It even extends to after you have completed the dungeon in the story; the final room of the dungeon can only be accessed from the Encephalon, and to open the door you must return to the last story room with your characters to activate a switch, and then go all the way back to your AMWS and up to the second floor to access the new room.
  • Tear Dryer: The ending of the anime sees two of Shion's close friends, Kirschwasser and KOS-MOS, sacrifice themselves for the rest of the group in short succession, leaving Shion bawling her eyes out in desperation. Just then, however, KOS-MOS emerges from the rubble, battered but fully operational, turning Shion's tears into those of bittersweet joy.
  • They Changed It, Now It Sucks!: A good deal of the problems with Episode II were the result of this. Several of the voice actors were changed, the art style was changed to a more realistic look, which is bad if you liked the old look, and the battle system was changed, probably for the worse due to the above mentioned scrappy mechanic. The drama with said changes was so bad, the admin of the fansite Zenosaga.com (who was the biggest fansite at the time) would ban anyone on the forums if that person defended the game.
    • The same thing was also said about the anime's voice actors - in part because some of the voice actors (namely Epcar) didn't even know they were dubbing it, and they would have happily reprised their roles.
  • Too Cool to Live: Jin, the Citan Expy, consistently portrayed as one of the coolest, if not the most cool main character, KOS-MOS nonwithstanding, dies fending off Gnosis to protect Chaos and Nephilim. Shortly thereafter, KOS-MOS, who is Nigh-Invulnerable in the first two games and has gotten an upgrade to become more powerful since, also consistently portrayed as one of the most badass and capable characters in the series, dies doing the same thing.
  • Unintentional Uncanny Valley: Both Episodes I and II fall into this from the opposite direction:
    • While the graphics for I were top-of-the-line for their time and praised for their high fidelity and good animation, just as many hammered the large-eyed anime art style for making the characters look doll-like and lifeless. While it somewhat works for some characters due to many of them being artificial in nature, they can still end up looking too disturbing.
    • In an attempt to correct for said criticisms, II shifted course by changing the art style to a very realistic one. While this resolved the glassy-eyed issue and was considered an improvement for some characters such as MOMO, for others like Shion and KOS-MOS it made them unrecognizable and just as creepy. Also, considering how big-eyed and distinct the designs were in the first game, the sudden jarring change was already bad enough, but as the characters still had an anime approach in their movements, their expressions just didn't look quite right as they often veered into Dull Surprise, and other problems that resulted in a clash of what the game wanted to be and what it actually was.
  • The Un-Twist: The identities of the Red and White Testaments, Kevin and Albedo, are foreshadowed with numerous heavy-handed hints and are both blindingly obvious by the end of Episode II. To smash the point home, their Episode III character art shows them both unmasked, obliterating any residual shock that would have come from The Reveal in the game itself.
  • Unintentionally Unsympathetic: However abusive their romance was, Kevin's love for Shion and desire to save her is portrayed as the sincere actions of a Well-Intentioned Extremist, and his ultimate betrayal of Wilhelm and Heroic Sacrifice for Shion's sake is meant to be the culmination of it all. However the sheer amount of dog-kicking he engaged in up to that point, including his emotional abuse of Shion, makes it hard for many fans to swallow what seemed to them to be a last-second and unearned change of heart.
  • What Do You Mean, It's Not Symbolic?:
    • Nephilim's necklace is in the shape of a cross, her name is a direct reference to the giants from the Bible who created the Great Flood... let's not get started on the symbolism behind the white and her possible relation to Elly.
    • Virgil was the name of Dante's guide from The Divine Comedy and the writer of The Aeneid.
  • Wangst: Most of the criticism against Shion in Episode III come from this. See Base-Breaking Character above.
  • The Woobie:
    • Momo tries to be cheerful even though she has a madman father, distant mother, and is perpetually tormented by her possession of the Y-Data. She definitely needs a hug.
    • Shion goes through a lot of trauma here, especially during Episode III and the arc on Old Miltia.
    • Cherenkov. It says something about how awful his life was when meeting Margulis was best thing to happen to him.
  • Woolseyism: How some view the removal of the blood in Episode I. The bone-crunching noises (combined with Albedo's head turning at an angle that clearly looks like his neck is broken) made many players even more unnerved.

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