Plot summary of Xenosaga Episode II

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This page describes a plot summary of Xenosaga Episode II - Jenseits von Gut und Böse. It is not a full description nor a complete novelization, but simply an overview of major events. If the reader is looking for a full script, see here.

Prologue

It is the height of the Miltian Conflict, as a Miltian ship gates out over Miltia, video footage show out of control combat Realians rioting in the streets. Lieutenant General Helmer sends Canaan a special Realian specifically created by Vector Industries's CEO, resistant from going out of control and chaos to the surface in their E.S. Asher. They make land down in the streets while fending off U-TIC craft and make their way to Labyrinthos. chaos reveals that their mission is to rescue the last remainig U.R.T.V.s and the Y-Data. En route, the Song of Nephilim activates, driving nearby Federation A.M.W.S. pilots insane, Canaan too almost succumbs to the Song but remained in control when an unaffected A.M.W.S. piloted by Jin Uzuki saves them. Jin reveals that he stole a data disc fron Margulis.

The two abandoned Asher and continued on foot where they were confronted by Colonel Margulis. Jin and Margulis duel and manages to wound one another, but in the end Margulis is defeated, sent plummeting to his doom. Jin decides to entrust the contents of the data disc to Canaan before going their separate ways. Canaan and chaos then observe a cloud of darkness approaching them before the footage is cut off.

Chapter 1

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Fourteen years later in the present, Canaan is undergoing memory examination at the Second Miltian Government offices, but hits a roadblock. Canaan is later summoned by Representative Helmer who reports in. Meanwhile, a man, the Patriarch, is reading a holy book, before his subordinate, Orgulla reports in regarding the Y-Data from chief Inquisitor Margulis. A hologram of Margulis then reports in, who is then berated by the Patriarch, who then explains himself, saying that Albedo that the Y-Data is secured by some form of high-level protection that can be only accessed by the U.M.N.. The Patriarch reveals that Cardinal Heinlein has manipulated the Federation's upper ranks, and asks him if he knows anything which he denies and assumes that it is the interest of the organization's best interest. The Patriarch is considering to invade the demilitarized zone in the future before Margulis before ending communications. Later, on his flagship, Margulis contacts Pellegri who sends Richard and Hermann after MOMO before Margulius authorized her to use the E.S. Issachar for the operation.

Meanwhile, picking off where Episode I has left off, as the party begins to descend into the Second Miltian spaceport, Shion (who later lost her glasses after Allen accidentally steps on them) narrates a recap of the previous game. After landing, the party go their separate ways, Shion, Allen and KOS-MOS heads to Vector Second Division while Jr., MOMO, chaos, and Ziggy make their way to the Government offices. On route, they are attacked by the U-TIC Organization, lead by Richard and Hermann in their A.M.W.S. Scutum and Pilum. Eventually they are cornered and Issachar, piloted by Pellegri attempts to capture MOMO but is driven off by Asher, piloted by Canaan with the Vessels of Anima reacting to each other.

Jr. thanks Canaan for saving them. who then explains to the party that Canaan was the one who rescued him and Gaignun after the Miltian Conflict when they were younger. In the said flashback, Jr. is carrying a dying Gaignun, begging for help, they were spotted by Asher, being piloted by chaos and Canaan who then picks carries them to safety. Since that day, Jr. owes chaos and Canaan their lives. At Vector's Second Division, Shion and Allen is informed by their superior that due to the increase of the Gnosis phenomenon, which resulted in the destruction of 120 star systems, KOS-MOS will be fitted with the Tertiary Weapons System as a last resort. After the meeting, Shion reminiscences about her and Kevin about KOS-MOS's birth and a craft designed to be used with her as a method to save mankind. After the flashback ends, Shion decides to explore the city before stopping at Moby Dick's Café.

Inside she meets her old employer, Boss who talks about old times. chaos and Jr. (with a new set of clothes) later stops by, much to her surprise. Meanwhile in the Government offices, Gaignun, Mary and Shelley meet up with Helmer and talks about their future goals. When the sisters left, Helmer delivers bad news: according to Lapis Roman, several U-TIC affiliates have begun showing signs of armed rebellion, causing Second Miltia be on full alert, warning Gaignun and the Kukai Foundation to be careful as well due to having the Zohar Emulators and MOMO in their possession, making them a prime target. Shelley then brings in MOMO who introduces herself to Helmer. Helmer and Gaignun remarks that she resembles a lot like Sakura. Helmer then tells her that she'll soon undergo analysis at the U.M.N. Control Center. Helmer then requests Gaignun to do reconnaissance.

After Gaignun steps out of the office, he telepathically communicates with Albedo (who is piloting E.S. Simeon at the time) Gaignun tries to persuade Albedo to stop, only for him to taunt the former with a quote by Paul McCartney and calls him an executioner. Gaignun denies it but Albedo guesses that he's with Jr. because he's waiting to fulfill his true mission. Once Albedo mentions that he's using Jr. Gaignun becomes agitated and cuts off the telepathic connection, obliterating Albedo's left arm (which grows back quickly). After the conversation, Gaignun realizes that Albedo intends to link up with U-DO no matter the consequences and questions why he wants Jr..

Back at Moby Dick's Café, Shion, chaos and Jr. are eating curry. and discuss their future plans together. When Jin arrives, Shion tries to hide from him and fails miserably. After Jin "greets" chaos, Jin and teases Shion, much to her chagrin. When Jin asks how long she was here, Shion excuses herself saying that she's busy. Jr. tries to interrupt, only for Shion to kick him in the knee. Shion then gets a call from Allen from her Connection Gear, telling her that the Tertiary Weapons System will take longer than expected, approximately about two or three days and ask her to take it easy for a while, much to Shion's dismay. Shion decides to reluctantly return home and Jin asks Jr. and chaos to tag along.

At the Uzuki residence, chaos and Jr. are awed on the antiqueness of the house. Shion is annoyed that Jin opened a bookstore instead of a doctor's office. Shion guesses that Jin got bored and changed professions. As Jr. and chaos rummage through the books, Jin tells her that minus mental illness, everyday illnesses can be cured now with medicine or nanotechnology. Shion then accuses him of using his hobby as an excuse of getting a tax break, questioning Jin how she got the books in the first place. Jin claims they were found in their grandfather's storage for years while the others are from customers.

Meanwhile aboard an Ormus ship, Sellers tells Margulis that he destroyed Pleroma, considering it was tainted by the Federation and "apologizes" for destroying a historical relic. Margulis reassures Sellers that the name was chosen by the Patriarch in his madness and couldn't care less. Margulis tells Pellegri that Albedo will soon release the seal on Old Miltia and the Patriarch will begin an invasion on the planet to acquire the original Zohar.

Back at the Uzuki residence, Jin pushes Shion to visit their parents' graves but adamantly refuses, pointing out that they were never buried there, angry that he let her parents die during the Miltian Conflict and walks out of the room. Before Jr. leaves for the U.M.N. Control Center, Jin apologizes to Jr. for Shion's outburst, while chaos decides to stay over tonight. On the porch at night, chaos and Jin talk about the U-TIC organization and the Miltian Conflict and their fate. Jin philosophies that humanity started out as hunter-gatherers how they obtain the power of the blade, and how the consciousness constantly changes form, comparing humans to moths before blocking a moth from approaching the candle. Jin then asks chaos to look after Shion, lamenting that he was unable to be there where she needed him the most.

The next day, Shion (with a change of clothes and new hairstyle) decides to go back to Vector Second Division to keep an eye of Allen and is worried about KOS-MOS and says goodbye to chaos and tells him to wish MOMO luck for her. chaos then makes his way to the U.M.N. Control Center. Jr. MOMO (with a new set of clothes and a beret), Ziggy and Gaignun (who is constantly checking his watch) waits for Juli Mizrahi. When she arrives, she acts surprising nice to MOMO. Juli then admits to Jr. that she was only nice because MOMO was designed to feel familial warmth. This agitates Jr., claiming that being cold and emotionless will wind out hurting her in the end. Juli says that she is frightened that MOMO was created by Joachim. Jr. then tells Joachim that he made a promise to Sakura, saying that he'll treat MOMO like a real human being, saying that she requested him to look after her and Juli. chaos then shows up and Juli leaves.

Ziggy takes notice of Juli's reluctance to interact with MOMO, which she claims that the various 100-series is a constant reminder of Sakura's death. Ziggy deduced that the 100-series looking like Sakura Joachim's idea which she confirms. Juli then asks if he had any family which he replies that he has a son who he lost in an "accident", citing the reason why he committed suicide 100 years ago. Juli ponder that she should've done the same when Sakura died but instead of grief, her heart is full of resentment towards her late husband. Ziggy suggests to Juli to imagine that she has two daughters: one has died and the other is still alive, telling her to consider it. Juli says she'll think about it before departing.

It is finally time for the MOMO's analysis, with Mary, and Ziggy watching over her. First, the 100-Series shut down her artificial personality layer, causing her to have a existential crisis. Helmer asks on the process, with Mary saying that the 100-Series are having a hard time preparing for MOMO's analysis due to her complex protection and damaged roots from the previous hack attempt. Mary laments that like they're doing something terrible to her, reminding her when she and her sister were used as guinea pigs back on Old Miltia. Suddenly, something goes wrong; the 100-Series analyzing MOMO suddenly collapses on their work stations as the alarms starting to blare. A trap laid by Albedo has been set off. Juli then tries to shut down MOMO, but is unable to bring herself to do so. Suddenly MOMO cuts off her neural pathways to protect the data inside her. MOMO then falls unconscious, as Juli applies CPR, Albedo gloats on screen about the trap he set, taunting the unconscious girl, calling her a puppet waiting for a miracle to make her human, before laughing manically before the transmission is cut off.

After the incident, Jr. and Helmer enlists Shion and Helmer in their assistance in recovering the Y-Data from her which they agree as she and MOMO are close friends. Meanwhile at the Federation Parliament, the senators bicker about the Immigrant Fleet deploying ships to Second Miltia. The Patriarch is given the chance to explain himself, claiming that the Immigrant Fleet are the original caretakers of the Zohar. A senator interrupts him, claiming that all Zohar activities are under Federation jurisdiction, accusing him of monopolizing the Zohar for himself. The Patriarch claims he wouldn't dream of it, saying there are others who are trying to claim it as their own, accusing Second Miltia of using the Miltian Conflict to justify their mobilization, accusing them of using Proto Merkabah to ignite war across the galaxy, using the chaos of war to use the Zohar for their own interest. And in response of the accused usurpers, he proposes to reclaim the Immigrant Fleet's right to be the caretaker of the Zohar. A senator corrects him that the incidents that Second Miltia is accused of is actually perpetrated by the U-TIC Organization, and they were cleared of all charges, citing the evidence provided by Vector Industries. Another senator claims that Vector is supported by Second Miltia, doubting how trustworthy the evidence is, asking where Helmer is right now.

Chapter 2

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Chapter 3

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Chapter 4

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Post-game

Just prior to heading to the Ω System, the party is approached by the Professor who asks them to head to Robot Academy. There he tells him his "true reason" he's dedicated to building giant robots: The Dark Professor (who claims to be his twin brother despite not being truly related) is planning to use Forbidden Devices for an evil scheme to rule the universe while constructing a giant robot of his own called Dark Erde Kaiser. He wants to defeat his rival's robot, he would gain respect and adoration throughout the galaxy, gain a country club membership, and save the universe. Despite his research, the Professor is unable to pinpoint the location of his rival and asks his colleague, the Other Professor in Second Miltia on finding him.

The party travels to Second Miltia to meet with the Other Professor in his apartment. There, he gives the party Sequencer B, allowing the party access to a yellow Forbidden Device. The party uses the yellow Forbidden Device at the simulation of the Ormus Stronghold where they find themselves at a Desert. There, they defeat its guardian and obtains Sequencer C, where they use the red Forbidden Device at a simulation of Sakura's subconscious, taking them to an abandoned factory. There, they come across a recently Gnosified victim who they put out of its misery and acquires Sequencer A. They then return to the Other Professor's apartment who grants them access to the green Forbidden Device, transporting them to an ancient temple in the sky. There, they battle through several Gnosis and defeats the temple's guardian and acquires Sequencer D.

After acquiring Sequencer D, they return to the Desert and activates the multicolored Forbidden Device, transporting the party to a Space Coliseum where the party and the Professor confronts the Dark Professor. There, the Dark Professors reveals his true motives: to conquer the Encephalon to take control of humans that use the U.M.N. before summoning Dark Erde Kaiser to battle the party. However, his opus magnum was destroyed, and the Dark Professor escapes, thus saving the universe from his evil schemes.