Voiced by Ai Maeda in Japanese and Lia Sargent (Episode I & III), Olivia Hack (Episode II), and Stephanie Wittels (anime) in English.
Shion is the iron-willed but fairly ditzy head of Vector Industries First R&D Division's KOS-MOS project. She is the character around whom most of the events of the games revolve. She is (arguably) the central protagonist of the series.
Action Girl: Shion is described as a very competent martial artist, though this really only shines in episode three. Put her in a AWGS, however, and she kicks all kind of ass regardless.
Badass Normal: She's the only vanilla human in the first game's party. She quickly crosses over into Badass Abnormal though.
Bunny-Ears Lawyer: Shion seems to be a pretty competent scientist when not needlessly risking her own life or forgetting important documents.
Cosmic Keystone: She has it for the entire series without ever knowing it.
Deus Angst Machina: So very, very much. See the trope page for the full story.
Custom Uniform: Shion's Vector uniform has blue highlights, unlike the green or red uniforms everyone else wears. Justified in that Kevin also wore a blue uniform, suggesting that blue denotes the project chief while everyone else in red and green are just regular members of the dev team.
Fear of Thunder: Understandable, since her nanny, parents, and lover were all brutally killed in front of her during two different thunderstorms.
Heroic BSOD: After finding out she's the one who called the Gnosis into the real number domain and summoned Abel's Arc.
Hot Scientist: Ironically, her attractiveness increases the further she drifts from her job, going from an awkward and nerdy woman who's shackled to her job in Episode I to a veritable (unemployed) fashion model in Episode III. Unfortunately, her mental faculties seem to regress somewhat to make up for it...
Improbable Age: She's the head of an extremely prestigious and cutting-edge research group belonging to the largest company in the galaxy while in her early twenties. And the average lifespan of humans in this universe is in hundreds of years. Probably justified in that Wilhelm needed her close so that he could keep track of her and make sure that she was in the right spot at the right time.
Mini Dress Of Power: Her Vector uniform in Episode I. It returns as an alternate outfit in III.
Pals With Jesus: Shion, in a past life, was called the Maiden of Mary. It seems that she and Mary Magdalene (yes, that Mary Magdalene) were very close.
Oblivious to Love: Allen tries to ask Shion out and/or just get across that he loves her several times in the series and she just doesn't get it. He finally gets the girl, only because he decided to stand up to Kevin to win her back from him. To think what would have happened if that never occured.
Tsundere: Particularly to her brother Jin, but also to just about everyone in her life other than KOS-MOS.
TV Genius: The alleged robotics genius, is thicker than a brick on an interpersonal level and says and does a lot of really dumb things throughout all three games. Most obvious in the third game.
KOS-MOS is an android built by Shion and Kevin Winicott in order to battle and destroy the Gnosis threat. She can use UMN transport to manifest absurdly powerful weapons. She is capable of generating the Hilbert effect (which draws Gnosis into Real space so they can be fought) at a range wider than even 100-series Realians can do with an amplifier. Her inner workings are described as a black box, and she sometimes acts in ways that go outside her programming.
Sealed Inside a Person-Shaped Can: The conscience of Mary Magdelene is stored within KOS-MOS and is used to oppose the power of Anima (should anything bad happen) whom is chaos.
Soul Jar: To T-Elos, to a degree. KOS-MOS' body was supposed to only be a temporary container of the Soul of Mary Magdalene, which was meant to be eventually absorbed by T-Elos.
Stripperific A constant across all her various bodies and outfits... and apparently in direct proportion to Shion's role in designing them.
White-Haired Pretty Girl: Her very light blue hair in Episode I and III definitely evokes the spirit of this trope. Not so much when it is darker blue in Episode II.
Zettai Ryouiki: All of her costumes except her optional swimsuit.
chaos
Voiced by Soichiro Hoshi in Japanese and Derek Stephen Prince (Episode I), Joshua Seth (Episode II & III), and Clint Bickham (anime) in English.
Chaos is a very mysterious young man working aboard the tramp freighter Elsa. He seems to have connections to Jr. and Jin that date back decades. He also has some sort of connection to KOS-MOS as well as the Testaments and Wilhelm. He can destroy Gnosis with a touch.
Anthropomorphic Personification: Of the power of Anima, a failsafe built into the Universe to destroy the "lower number domain" (the "real" universe) if the dispersal of consciousness ever threatened to destroy the "upper number domain." Naturally, chaos doesn't really want to do that.
Beware the Nice Ones: The nice guy of the series. Also the one with the power to destroy Gnosis with a touch. And is an immortal, and implied to be the one behind Jesus' miracles. Oh, and he's the harbringer of the Apocalypse, if it ever comes to that.
Blessed with Suck: His power of Anima is to ensure that the dissipation of the Collective Unconscious doesn't engulf both the Upper and Lower Domain and destroy the universe. While this sounds all well and good, the alternative is that his power actually Only contains the dissipation inside the Lower Domain, that is, the world the characters live in and the world where the Collective Unconscious reside, meaning, the Lower Domain is sacrificed to save the Upper Domain.
Heroic Neutral: He acts like a Bad Ass Bystander during the majority of the plot (with only a declaration of...something at the end of Episode 2) and only reveals his full power at the end.
Kung-Fu Jesus: This is almost as literal a case you can get. He fights with his fists and was the Man Behind the Man to Jesus. i.e. chaos did Jesus' miracles while Jesus got the credit. Also, Wilhelm once called chaos "Yeshua," a name which, in some circles, is synonymous with Jesus.
The Man Behind the Man: Inverted: Chaos is supposedly the man who worked the miracles for "The Messiah" (read: Jesus) while said Messiah was the public figure who everyone thought was doing them. Not really all that evil.
Really 700 Years Old: Or Time Abyss. He's been around since Jesus, making him at least 7000 years old. (Xenosaga taking place almost 5000 years after present day.)
The Stoic: He doesn't emote much. It's especially jarring when KOS-MOS awakens as Mary and he...just...stands there. And he's supposed to be Mary's soulmate.
Ziggurat 8, dubbed "Ziggy" by MOMO, was a police man named Jan Sauer in life. He committed suicide after losing his wife and child and was resurrected as a cyborg. He was hired to rescue MOMO from the U-TIC organization. He seeks to have all the organic parts of his brain replaced with machines so he can finally die. Eventually becomes a father figure to MOMO.
Cyborg: He is one, but is considered obsolete by the time the series starts. Doesn't stop him from kicking ass all over the place.
Expy: Ziggy has a great deal in common with Robocop, from the Robo Cam to denying his previous identity until after some Character Development, and also looks more than a bit like Rutger Hauer as Roy Batty.
Hammerspace: Presumably he uses UMN transport for his BFGs, just like KOS-MOS.
Not So Stoic: After he sees Voyager in Episode II, we get to see him get pissed. Which leads to...
Hypocritical Humor: Invoked by Jr. Ziggy spends a lot of time lecturing Jr to never let his emotions get the better of him during a high stress situation.
Take a Third Option: At the end of Pied Piper, Voyager offers Jan the choice of becoming a Testament like him, or being absorbed into his consciousness like all his other victims. Jan puts his service pistol to his head and blows his brains out.
To Become Human: Inverted. Ziggy is a human who wants to become a machine.
Eventually subverted. He stops his mechanizing after some Character Development from meeting MOMO and finding out Voyager is alive.
MOMO is the prototype 100-series Realian (a type of organic android) who is widely sought after for the data her "father," Joachim Mizrahi, left inside her. She regards council member Juli Mizrahi as her mother and is visibly distressed when her mother doesn't want anything to do with her. She has the appearance of a 12-year-old girl.
Age Inappropriate Dress: Her Episode I outfit is prone to giving the viewer many a Panty Shot and she's twelve. She may be a Realian, but still.
Apologetic Attacker: Episode I only. "I'm sorry, are you okay?" is one of her standard battle ending phrases.
Cherry Blossom Girl: She's based on Sakura Mizrahi, who is strongly associated with Death (since she was a terminally Ill Girl and Posthumous Character) and who was Jr.'s first love interest. MOMO's pink hair and status as a White Magician Girl (at least in the first two games) seems to be a reference to this trope.
Daddy's Girl: MOMO is really fond of her father, from what she can remember of him. She doesn't believe the rumors of his insanity when they pop up, even when they're seen as the common opinion. It is believed (even by her sisters) that she was Joachim's favorite.
Fun with Acronyms: Her name means 'Multiple Observative Mimetic Organicus'.
Magical Girl: In Episode I, MOMO has in-battle Transformation Sequences that give her special abilities. Seriously. Her name is also a Shout Out to a classic magical girl, Minky Momo.
Magic Knight: Due to gameplay mechanics in Episode III, she can be the best at dealing the most single target physical damage of all playable characters, even if her actual strength is actually dishing magical attacks and heals. Of course, she's not able to take damage as well as other characters, and takes certain gearing to bring her to average defensive wise.
Mind Rape: By Albedo. Went to absurd lengths to try to remove the "mind" part.
Muscles Are Meaningless: One of her techs in Xenosaga III is her own version of Ziggy's basic attack, Sword Fish, identical in animation and name. Since it does more damage and includes a heavy breaking effect, this pretty much reveals that MOMO punches harder than Ziggy. Mull that one over. Possibly justified by her being a super-advanced Realian.
Replacement Goldfish: To Ziggy for his dead child, presumably to Joachim for his daughter Sakura, and possibly to Jr. for Sakura.
Joachim and, eventually, Juli come to see her as a second daughter than a Replacement Goldfish for Sakura. It's even mentioned that their personalities are very different.
The Straight and Arrow Path: Since her bow channels Ether energy, and she is an ether attacker in almost all of her skill paths, the bow actually is a better choice for a weapon than a more "modern" weapon, at least in game logic.
To Become Human: Dr. Mizrahi told her that if she did many good deeds, she'd become a real person.
Indeed, she gets closer than most after the end of Episode III - the Encyclopedia mentions that she gained an upgrade that would allow her to carry a child.
White Magician Girl: Fits to a T in the first game, being primarily a support character, very feminine, a Mysterious Waif, and wielding a rod. Her skillset is player defined in the second, and in the third, you can choose to make her a Black Mage or a break attacker.
A gung-ho young man who commands the starship Durandal. He is second in command of the powerful Kukai Foundation, although his exact relationship to the owner, Gaignun, is the matter of some speculation. His weapon of choice is antique dual pistols.
Adorably Precocious Child: He looks like he's in his preteens, but acts much more mature. His design is obviously intended to play up the cute aspect of this. However, it's later revealed that he's actually immature for his chronological age, which somewhere around 30.
Artificial Human: Jr. is a URTV, a human specifically designed and created to fight U-DO.
Badass Longcoat: In Episode I and Episode II. In Episode III he gets a Badass Shortcoat.
Bond One-Liner: Usually as part of his victory pose after battle:
Episode I: "Sayonara, baby!"
Episode II: "I'll be sure to send you some flowers."
Expy: He has the same weapons and similar attacks to Billy Lee Black from Xenogears, which may also be where his religiously-themed clothing and Angelic Requiem attacks come from. His personality and role, however, is closer to Bart.
Really 700 Years Old / Never Grew Up: Jr's powers have frozen his physical age in his late preteens or early teens. He's really in his twenties and the oldest of the variants (including Gaignun). It's also implied he can live as long as he wants, having The Ageless type Immortality.
Twin Telepathy: Between all the remaining URTVs, but especially strong with his formerly conjoined twin, Albedo.
Warrior Poet: Jr. likes to quote from books, which are considered antiques by Xenosaga's time. One 4Koma pokes fun at this by having Allen being bewildered at how to even start reading one.
Young Gun: In addition to being The Gunslinger, Jr. completely fits this role as well. He's both, because he is actually over twenty years old and is definitely experienced enough to be an actual gunslinger. However, since he looks and acts like a typical Young Gun, he fits this too. The only difference is that he's not attached to any sort of older mentor.
Jin Uzuki
Voiced by Crispin Freeman (Episode I), Michael Gough (Episode II & III), and Chris Ayres (anime) in English.
Shion's brother, a slacker who abandoned medical practice shortly after completing his training and bounces from obsession to obsession. He currently runs a book shop full of actual paper books, which baffles and infuriates Shion. He has a history with chaos, and was deeply involved with the incident on Old Miltia that led to it being sealed away.
Badass Bookworm: Jin is this to the point that he owns his own bookstore. Jr. is a subversion of this. He loves reading to the point where he still caries around paper books in an age where they're considered antique (and acting like a kid in a candy store with Jin's bookstore), but is also very emotional and Trigger Happy.
Badass Normal: Jin is perhaps the only "normal" human in the group, and only KOS-MOS can rival him at being the biggest badass.
BFS: Subverted by his normal sized katana in melee combat, but played dead straight while in his ES (giant mecha).
Charles Atlas Superpower: Jin can slice through giant mecha with a sword, while ostensibly being a normal human.
Shion: What do you want? Are you here to say a bunch of cryptic things again and confuse me? You're always like that. You just appear in front of me, say whatever you feel like, then just watch without actually doing anything!
Expy: She looks remarkably like Elly from Xenogears. Given the ending with her and Abel, this was probably very deliberate.
Meaningful Name: Nephilim means "watchers" or "those who have come down."
Theme Naming: Nephilim's name follows along nicely with Albedo and the other Testaments.
Virtual Ghost: Made possible since the consciousness of the dead can be found within the UMN.
What Do You Mean, It's Not Symbolic?: Her 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.
Can Not Spit It Out: He has a crush on Shion, but can't work up the nerve to tell her. Justified: Shion hasn't had the nicest of lives, especially with people that are close to her. He's afraid that in getting close to her, he'll end up hurting her more by reopening old wounds or otherwise. When he ''does'' work up the courage to say it, however...
Voiced by Emi Uwagawa in Japanese and Michelle Ruff (Episode I) and Heather Hogan (Episode II & III) in English.
Miyuki is a systems programmer for Vector and an amateur inventor. She is very fond of Shion and goes out of her way to help her out with her inventions when she can.
Flanderization: She suffers from this horribly in the third game, turning her into a Butt Monkeyditz with everyone showing little faith in her doing ANYTHING right and treating her pretty horrible as a result, especially by Shion.
Gadgeteer Genius: Of a slightly toned down variety. She's invents all of Shion's MWSs, including her Infinity+1 Sword version, plus KOS-MOS's Infinity Plus OneScythe in Episode I. Her hobby is sending off patent applications to the Federation Patent Office.
The former head of the Third Division, KOS-MOS's original designer, and Shion's fiance. Deceased at the time the game opens. Or so you are meant to think. He orchestrated his own demise at the hands of the KOS-MOS archetype in order to become a Testament and help Wilhelm. His reasons for doing so is so that his time with Shion can last forever.
The Dog Bites Back: He betrays Wilhelm only when said Big Badstarts to tell him how much he failed at his role in his Xanatos Gambit and tortures Shion by karate chopping his arm off. When that doesn't work, he literally stabs Wilhelm In the Back, killing the both of them, so the party can save the universe.
Used to Be a Sweet Kid: Subverted to hell and back: He was a rotten, duplicitous little bastard even as a kid. Heck, he used to be a bad kid by comparison because at least he was a lot better at hiding it as an adult.
Rank Lieutenant. He is a A.G.W.S. pilot stationed on the Woglinde and a veteran of the Miltian Conflict. A Jerkass who actively insults Shion's optimism and belief that Realians count as people. Is eventually killed by KOS-MOS because he kept getting in line of her fire.Or he would have if he wasn't brought back by Wilhelm. He then becomes the Blue Testament, personality intact. His reason for becoming a Testament is tied into the Miltian Conflict. During the period, he lost his whole squad to Realians and would have died if he didn't get a transplant from a Realian named Febronia, who also took care of Shion. While recovering, the formerly hard-assed soldier eventually softens and the two fall in love. However, when all things went to hell, Febronia died. He blames himself for being too weak and not being able to protect her. Because of this, he rejected love and developed an intense hatred towards Realians. The reason he hates Shion's optimism so much is because she reminds him of Febronia.
Jerkass Woobie: Febronia, the woman who ignored the fact that he was on a mission to kill Realians like her, donated her organs to save his life, and the two fell in love... and she got eaten by berserk Asura-series Realians straight from the Uncanny Valley right in front of him as he lay helpless.
Love Redeems: He meets Febronia again during the events of Episode III. He initially rejects her due to his guilt but eventually relents when she tells him she still loves him regardless. A Crowning Moment of Heartwarming and a Tear Jerker.
Not so Different: Between him and Shion. One way he tries to break her optimism.
Schrödinger's Cast: In Xenosaga: The Animation, Virgil survives the attack on the Woglinde in place of Commander Cherenkov, only to be killed later by KOS-MOS (for the same reason as in the game).
Tony's childhood friend and the navigator of the Elsa. His hacking skills are reportedly top-notch, and Vector has tried repeatedly to hire him.
Expy: Of Hammer from Xenogears, minus the anthromorphic rat aspects.
Playful Hacker: So good that Vector scouted him but he always declined.
Mary and Shelley
A pair of sisters rescued from cruel experimentation by a pharmaceutical company by the Kukai foundation. They serve as Gaignun and Jr.'s secretaries and seconds-in-command.
Break the Cutie: Their back story before Gaignun rescued them.
Meaningful Name: They are named after Mary Shelley, the author of Frankenstein. Which makes sense, considering the cybernetic and genetic modifications done to them.
Pronounced "oo-doo". It's an acronym for Unus-Mundus Drive Operation. Despite the deception, it is not a computer program.An indescribably powerful and alien entity, U-DO is an Energy Being that lives in UMN space, discovered by Dimitri Yuriev. Able to drive people insanethrough mental contact alone, it is a malevolent creature with no regard for humans... Except for the part where all that turns out to be boldface fabrications by Yuriev. While it does drive people insane-see Albedo-this is mostly accidental on it's part. In reality, it is the sentient avatar of the mind of the universe, a Gnostic God who possesses a benign, scientific interest in humans. Unfortunately, it's mind is so powerful it literally destroys the minds of most people it attempts to contact. As shown throughout it's interviews with Shion in game #3, it seeks to understand the goals and psychology of humans and the nature of the universe. To do that, it created two observational units-Abel, a FeiExpy who gathers information in physical space, and Abel's Ark, a colossal-star system sized-living ship who observes spiritual space. It is an important element in all three games.
Brown Note / Mind Rape: Coming into contact with U-DO has this effect. The exact effects is the individual learning what U-DO has seen. Namely, isolation enough to drive a person mad and the end of the universe.
Cool Ship: Abel's Ark, which is absolutely fuggin' huge, having a solar system as an interior decoration
Counterpart Comparison: In-universe example. Since Abel's Ark lives in the same spiritual dimension as the Gnosis, people initially assume it to be a Gnosis Mother Ship like the Cathedral Ship.
Cosmic Horror: Subverted. It's simply a completely alien existence from a higher dimension. And it's curious about humans in a scientific way.
The extremely creepy and Axe Crazy recurring villain who delights in tormenting Jr. He has an obsession with MOMO that goes above and beyond seeking the data locked inside her.
Ax Crazy: And then some. Also one of the most pure examples of "crazy" in media. Most of the time, Ax Crazy is simply extremely vicious sociopaths with little regard to human life. Albedo personifies the truly insane elements by making semi-coherent references to various works, often randomly and with the loose relevance to the current issue and has a warped pattern of speech ("I am the ultimate telomerase!" when he's referencing his immortality). To be fair, though, this is due to being corrupted by U-DO.
Back from the Dead: No less than three times in Episode II, for a given amount of "dead."
Death Seeker: All he thinks he wants is for Jr. to kill him at last.
Drunk on the Dark Side: Albedo firing Proto Merkabah at Second Militia definitely qualifies. Also, this trope is a part of what he wants, overall, since he wants to link up with U-DO again so badly. Also, commenting on his first link up with U-DO...
Albedo: I experienced but a fragment of my true power that day. The waves that inundated my body, are now apart of me. I've reached a higher stage of existence, compared to you incomplete mortals. I am the Alpha AND the Omega of perfect consciousness!
Evil Laugh: Albedo's even dwarfs Kefka's in sheer insanity. Kefka's was jolly, jovial wickedness. Albedo's is the kind of thing you'd expect to hear in a mental institution. It's safe to say Albedo's runs laps around Kefka's and has energy (and lunacy) to spare.
Evil Twin / Cloning Blues: To Jr. More-so than Gaignun as Jr. and Albedo were conjoined twins.
Evil Tastes Good: "Feed me your hostility! Pierce me with your hatred!"
Go Mad from the Revelation/Freak Out: Twice; first one was when he learned that his brothers lack his infinite regeneration and could die, and the second is when he came into contact with U-DO.
Large Ham: The hammiest character in the series, bar none.
Lolicon: Has a disturbing fixation on MOMO and her Kirschwasser sisters eventually revealed because MOMO was based on Sakura, whom Jr. had a crush on. It's up to anyone's guess how much of this is him having a fetish, him trying to get Jr. to hate him, him being jealous of Sakura, or some combination of the above.
Mind Rape: Is very fond of this when around MOMO and Jr.
Nietzsche Wannabe: Justified. You'd be pretty damn nihilistic too if you were so unkillable that'd you'd get to see the heat death of the universe first-hand and got a preview of it from the local Cosmic Horror.
Noble Demon: While he doesn't pull a full-on Heel Face Turn, he does just as much good for the party as he does acts of indiscriminate evil. This is most evident as the White Testament.
Omnicidal Maniac: Albedo tries to blow up a planet. When that gets foiled, he just tries to drop the giant space station on it. However, this all may have been an act to get Jr hate him enough to kill him, as Jr is the only one who actually can neutralize U-DO's waves. Albedo would prefer getting killed than watch his brothers, mainly Jr, die.
Psycho for Hire: Though this trope alone wouldn't encompass his craziness.
Redemption Equals Death: He does this three times and every time it looks like he's gone for good, however, he just won't stay dead— He's molecularly reassembled by the Testaments, killed again by Jr., brought back as a Testament himself and dies again when his mind is absorbed by Jr. and his body is obliterated.
Terms of Endangerment: His frequent referral to MOMO as Ma belle péche or a variant of said phrase.
Twin Telepathy: Although all the URTVs can communicate telepathically, the link between Jr. and Albedo is especially strong, with Jr. even able to sense when Albedo is reduced to particles.
Who Wants to Live Forever?: Albedo has infinite regeneration, meaning he absolutely cannot die. Even if he is reduced to mere particles. Needless to say, upon learning that his brothers lack this regeneration, he takes it very badly. It Got Worse after contact with U-DO.
Wicked Cultured: Tosses literary references left and right in some of his more prominent scenes. Played with too; the way he makes references doesn't make him seem so much as "cultured" as completely insane.
The Grand Inquisitor of the Ormus religion, Margulis is ultimately only answerable to the Ormus Pope. He seeks the Zohar as a source of power and a relic of his religion. He is driven by a fiery faith, which ultimately burns himself as often as it smites his enemies.
Better to Die than Be Killed: To Jin, despite the fact that Jin didn't really want to kill Margulis in the first place.
Dragon-in-Chief: He's always second-in-command to the leader of Ormus, whoever it maybe from one moment to the next, yet he's always the one giving the orders. Until he suddenly isn't.
Even Evil Has Standards: He apparently has a distaste for torture, since he refers to Albedo as having "perverse taste in hobbies." Well, it's either torture or the...other...things that Albedo does.
Evil Counterpart / Foil: To Jin. Compare their styles: Jin fights without losing his cool while Margulis fights like The Berserker. Jin uses a Katana while Margulis uses a straight double-edged sword. During their dual, Margulis seems to have superior physical prowess while Jin is better at Ether-based attacks. Jin, and Shion by extension, have the blood of the People of the Zohar, which qualifies them to join Ormus. Jin didn't join while Margulis whole-heartedly embraced Ormus' teachings.
Evil Redhead: In the more realistic almost brownish-red style.
Gray and Gray Morality: Margulis is not strictly evil, and his greivences with the Federation are legitimate, especially the destruction of Michtam.
Omnicidal Maniac: He destroyed (well, actually gnostified) an entire planet of several billion people in order to conduct Zohar link experiments. He doesn't seem to care, either, stating that the inhabitants were of no use to anyone.
Voiced by Chikao Ōtsuka in Japanese and Michael Bell in English.
In public, Patriarch Sergius is the head of the galaxy's largest quasi-legal religion, the Immigrant Fleet, in private he's also the head of Ormus, the galaxy's largest religious terrorist cult. He is the immediate superior to much of the series's antagonists, namely Margulis, Pellegri, Sellers, and Heinlien.
Earth-Shattering Kaboom: He destroys Old Miltia by having the Ω System rip its way out of the planet's crust. Though Milita was uninhabited at the time, he is responsible for the largest amount of physical damage of all the villains until Wilhelm kicks off the Apocalypse at the end of Episode III.
Everyone Calls Him Barkeep: In Episode II, anyway. Margulis mentions him by name only in passing in Episode III.
Evil Old Folks: He is the oldest-looking character in the series. The chronologically-oldest characters have him beat by gigayears. One of them is in your party, and has been alive since at least Jesus' time.
First Church of Mecha: Ormus worships the Zohar as a holy relic and uses numerous religious-themed Humongous Mechas as part of their arsenal, including one that actually is a church. And then there's his own personal Deus Est Machina: Proto-Ω.
Light is Not Good: Dresses all in white? Check. Head of a major religion? Check. Light-based attacks? Check. Army of angelic super robots? Check. Base of operations looks like a space cathedral? Check. Genocidal tendencies? Double check.
One-Scene Wonder: Although he's the primary antagonist of Episode II, he's a blip on the radar in the series as a whole.
The head of Vector Industries, the largest corporation in existence. It is also revealed that he heads up the second largest company, Hyams and the religious organization Ormus. He has some sort of connection to chaos (the guy) and commands the Testaments.
The Chessmaster: So much so that other chessmasters could learn from him.
Creepy Monotone: He speaks only in a monotone. He is never shown to do anything else. Your Mileage May Vary on whether or not it's that creepy. Which can lead to...
Deus ex Machina: He acted as one for the protagonists in the ending sequence. Because the UMN had shut down, they had no way of getting away from Michtam quickly enough. Wilhelm created a gate so they could.
Fiction 500: He may be one of the wealthiest characters in the history of fiction, owning a company whose headquarters qualifies as an artificial planet.
Interestingly enough, he actually manages to subvert the more prominent elements of this in a roundabout way. To note:
Despite his status of being the CEO of Vector, very few people even seem to be aware of him (let alone of him having any status of being rich). For all intents and purposes, his office (which is a small room) on the Dammerung seems to double as his "house."
He is rarely (if ever) seen buying anything for personal want (let alone things that would have insane prices).
He funds things in his interest under the name of "Vector" rather than personally funding. This is a fair bit believable given Vector's history, scope and size. On the other hand, whenever he needs something built, he simply uses the various divisions of Vector and manipulates events in such a way that the products built have seemingly little to no relation to him. The stuff built is all relatively possible given the science used in the verse.
The only times he defies physics is when he's literally defying the laws of physics, which never has anything to do with money or Rule of Funny/Cool.
Gambit Roulette: This may be one of the very few times this trope is justified, since he has possession of a device called the Compass of Order and Chaos, which shows him the movements of consciousness. Being several thousand years old probably doesn't hurt, either.
He also has practically absolute control over the economy due to being the CEO of Vector and Hyams, as well as being a high-ranking Cardinal in Ormus. He was also head of the government a decade before the game takes place, giving him significant clout with the Federation.
Lean and Mean: Compared to contemporaries in the Xenosaga rogues gallery, he's a little on the thin side.
The Man: He fits this, considering that he runs/ran, at the very least we know of, two rivaling companies (Vector and Hyams), Ormus, and at least one of the Militian government's Subcommities.
The Stoic: If he has any emotions, the best we'll ever hear of it is him literally stating it.
Time Abyss: He is at least 4000 years old and probably a lot older than that.
The Übermensch: Considering the Nietzsche subtitles and that Nietzsche's middle name was Wilhelm, this is not surprising.
Blue and Orange Morality: He exists solely to prevent the destruction of the Lower Domain. He does not care for how many lives must be lost to achieve this goal.
Ironically, blue and orange are the colors of chaos' outfit in Episode I.
Wicked Cultured: Likes to refer to all the events happening as if it were an opera, apparently listens to Wagner a lot, is never seen in anything other than a plain business suit and plays chess. Apparently, a whole freaking lot. He also has some elaborate and poetic titles for certain people and features ("shining wills" and refers to the White Testament as the "Weaver of the Eternal Circle of Zarathustra").
Margulus' subordinate within Ormus. Unlike her superior, she seems to have flashes of conscience about the pathsthey walk, but not enough to make her reconsider her choices. She has a past with Jin.
President Evil: It's not explained very well in-game, but in the gap between Episodes II and III he has the Salvator faction stage a coup and install him as the Executive Committee Director of the Galaxy Federation.
Voiced by Rena Mizuki in Japanese and Erin Fitzgerald and Stephanie Mitchell (child) in English.
URTV #668, the missing unit between 667 (Albedo) and 669 (Nigredo). One of very few female URTVs produced by the Yuriev Institute, she was groomed from childhood to be Yuriev's personal aide and pointwoman for the Salvator Faction.
The Baroness: She's about as close as Xenosaga gets to this trope.
Voiced by Masaharu Satou in Japanese and Steve Blum in English.
One of the brightest scientific minds in the post-Miltian Conflict galaxy. Dr. Sellers is known as much for his intellect as he is for his shifting loyalties.
Early-Bird Cameo: He's not even named in-game when he shows up in Episode I for a minute or two. His proper introduction comes at the start of Episode II.
One-Scene Wonder: He's one of the principle villains of the story, yet his actual screen time is really quite minimal compared to Margulis, Yuriev, and the Testaments.
The Unfought: In a rare twist, the party battles its way into the heart of the Merkabah to confront Sellers only for him lecture them about what what idiots they've been and then just float away in his hoverchair.
You Are Too Late: He whips this out only after the fact, telling the party that while they've wasted their time battling their way through Merkabah, Yuriev has invaded The Durandal, and they're probably too late to do anything about it.
Voyager
Voiced by Kouji Tsujitani in Japanese and DC Douglas in English.
The black testament, who has some sort of connection with Ziggy.
The Cracker: Before he became a supernatural monster he was a Ghost in the Shell-inspired cyber-terrorist with whom Ziggy tangled during his days as a policeman.
Voiced by Mariko Suzuki in Japanese and Bridget Hoffman in English.
A humanoid weapon system built on the same principles as KOS-MOS, and vastly more powerful. She states that she must destroy KOS-MOS in order to be complete.
A.I. Is a Crapshoot: T-elos is cruel and sadistic, compared to KOS-MOS's logical indifference or protectiveness.
This could be more of the below Evil Counterpart. It's not just their personalities that's flipped, but pretty much everything along with a play on words. KOS-MOS is right-handed (dextrous, implying skill and effectiveness) while T-elos is left (sinister, implying cruelty. Obviously).
Evil Counterpart: To KOS-MOS, although it's a little more complicated than that.
Hollywoodyborg: Unlike KOS-MOS, who is a robot powered by Mary's soul, T-elos is a cyborg created from Mary's corpse, recovered from a time-displaced French tomb, but controlled by completely artificial computer brain.