One year after the events of Jenseits von Gut und Boese, the cast of Xenosaga find themselves each dealing with their own seperate demons. Allen is still lost regarding his feelings for Shion, as evidenced when they have dinner together. To try and express to Shion what he feels, Allen asks MOMO to help him choose a gift for Shion, which he later gives to her.
Meanwhile, a strange girl named Maria Niwashiro appears on Juli Mizrahi's doorstep. In conversation with MOMO, Maria notes that she once knew Sakura Mizrahi and that she and Juli were somehow related. Previously Maria and Shion had met on the UMN and met in person. Shion invites both Maria and Maria's friend from back home, the bubbly Roslin Orthas, to her reunion party. Juli, unfortunately, misses the party but meets up with MOMO and Ziggy later.
In the meantime, Allen strugges with his feelings, aided by Azuka Kasim, a Realian girl with a mysterious secret. At the same time, the rivalry between Albedo and Jr. heats up.
Confused over Azuka's masquerading as Shion, Allen attempts to find answers, while Shion shows Roslin around Miltia. Meanwhile, MOMO, Ziggy, Juli, and Maria spend a day together.
Back at the Durandal, Jr. and Gaignun discuss recent events with Helmer. At the same time, in a surprise move, Shion quits her job at Vector. Roslin and Maria explore Miltia together, and end up getting drunk. Roslin reveals her ties to the organization Scientia, and Maria offers to ask Juli to help her. To help, Juli takes Roslin in and gives her what help she can.
Faced with Shion's surprising exit from Vector, she and Allen have an argument. Shion leaves to begin work on the Durandal. Later, Shion meets with Ziggy, who is dealing with the realization that he's falling hard for Juli Mizrahi. Afterward, he finally gets up the nerve to tell her, although her response is ambiguous.
Albedo showed up to cause trouble shortly after. During their confrontation, questions were raised. Who is Albedo targeting? Why does Maria Niwashiro hate men? Will Allen, who is injured, survive?
After the Confrontation, everyone arrives safely on the Durandal. Allen, unfortnately, is stuck in a coma. When he wakes up, he is surprised to see Shion there--along with her new boyfriend. Shion and MOMO take time to visit the 100-Series Realians, while Allen meets with chaos in a dream. Later, he and Shion discuss the future of their relationship.
Maria Niwashiro had been heartbroken for years over the assumed death of her childhood friend and juvenile love interest, Citrine. So she's shocked when she runs into Citrine on the Durandal. Citrine reveals to Maria that she's dying of a degenerative disease and needs help from Yuriev to survive. While Maria struggles with this news, MOMO meets a strange 100-Series Realian named Azuka Kasim, who reveals that she's the result of an experiment designed to fuse two 100-series together. She also doesn't seem too fond of MOMO. Afterward, MOMO has a heart-to-heart with Ziggy.
Having learned that his dear sister was back--and looking for him--Gaignun gets drunk with Jr. Later, Citrine arrives and ends up beating Gaignun up in an attempt to release Yuriev. After failing in her attempt, Citrine ends up nursed by Maria.
In the meantime, Juli and Ziggy deal with issues of jealousy. Later, Juli meets with Maria, MOMO, and Roslin, who are all busy debating her love life. Allen's feelings for Azuka begin to take shape when she takes him home from the hospital, and Shion offers further advice to Ziggy. Later, he gets up the nerve to tell MOMO about his feelings for her mother, and Juli disloses just how much she dislikes Sharon Sauer.
Having left her job on Michtam, Roslin decides to seek out work on the Foundation, where she runs into Gaignun and they share a drunken kiss. Back at the Durandal, Azuka helps Allen face who he truly is. Meanwhile, Maria runs into Ziggy and offers him some much-needed advice. Just after, he takes her advice and he and Juli share their first kiss. Maria leaves to accompany Citrine to visit Roslin and coerce her into returning to Scientia. And back at Vector, the arrival of Rote Mantel and his T-ELOS project stirs up trouble.
Later, Juli and Ziggy spend an afternoon together. It's interrupted when Maria runs in to alert them that Shion has been lost inside the Encephalon. Juli acts as dive facilitator and Shion, Allen, Maria, MOMO, Ziggy, and Roslin all make an Encephalon dive.
But this isn't easy for any of the divers. First, they are faced with Maria's resonant memories. Here, they learn that Maria is Yuriev's creation, a URTV prototype created with the genes of Juli Mizrahi. They also witness Maria's final moments as a geisha, and learn that she was thrown out of the geisha district for being unable to overcome drug addiction, and for having an affair with another female geisha.
Next, Ziggy's past--and his links to Roslin--are exposed. Inside his resonant memories, the cast learned about how he became who he is, how Scientia was formed by Roslin's great-grandmother Meris, and just how much Ziggy's new family means to him. Nephilim makes a reappearance, with a cryptic message for everyone, before the dive ends and everyone is returned--thankfully, in one piece.
The night after the Encephalon dive, Ziggy finds Maria attempting to drown her sorrows in drug abuse. The next day, Roslin runs into Gaignun again, making for drama, as usual. Still upset over Gaignun's reaction to their kiss, Roslin gives Gaignun a chance to explain himself.
To celebrate Maria's 29th birthday, Citrine makes a special dinner for her, with the consummation of their feelings for each other for dessert. While Maria and Citrine get down, Roslin and Shion find a gift for Allen. Later, Roslin meets up with Ziggy, and they discuss Roslin's decision to take over Scientia or not. Ziggy spends an afternoon with MOMO, while Allen and Azuka also spend time together. Later that night, Roslin and Maria have a good cry on one another's shoulders.
Surprisingly enough, a rejected Shion tries to seduce Allen. The next day, Allen and Azuka's father, Kisaragi Kasim, discuss Allen and Azuka's relationship.
Juli and Gaignun learn that they've been called away to a government conference, and Ziggy prepares to accompany Roslin to Michtam to reconcile with her parents. Before being separated, Juli and Ziggy say a very, very fond farewell.
The cast is separated. Juli and Gaignun travel together to the Conference on Gedalya, and share some enlightening details about their pasts. Ziggy, Roslin, and MOMO head to Michtam, and one member of the party has trouble keeping focused. On the way to their respective destinations, Roslin and Gaignun chat via the UMN.
On Michtam, Roslin has some initial difficulties with her parents. Later, she and her father reconcile, and also dig up some important articles of Ziggy's past.
In order to make a very boring conference a bit more interesting, Juli and Gaignun break out the alcohol. Meanwhile, Shion is reunited with Jin.
Back at Scientia, Natasha and Boris Orthas give Roslin a second chance, asking her to infiltrate the conference. Ziggy calls Juli to tell her he'll be on Gedalya. Afterward, he discusses his future with Boris Orthas.
Meanwhile, Citrine and Maria also infiltrate the conference. When Juli and Maria see each other, their latent hatred of one another is revealed as they lash out.
Trouble erupts all at once.
Ziggy and MOMO are hiding in a warehouse, waiting for Roslin, when Voyager arrives. Voyager ends up causing an explosion that leads to Ziggy being charged with terrorism and held at a Gedalya prison. Citrine attempts to infiltrate the building, but is detained by reporters. In the meantime, Roslin makes plans to rescue Ziggy as well.
After having seen one another at the Conference, Maria and Juli have an extremely violent fight, and reveal some shocking information concerning their pasts. In the meantime, Shion and Tony have a random hookup. In addition, MOMO tells Juli what's just happened. Upset, Juli visits Ziggy in jail. In their own "special" way, they discuss the possibility of getting married.
Back at the Scientia hideout, Roslin and her parents discuss tactics for a jail break. Citrine brings Maria back, and she and Natasha Orthas realize that they were both geisha from the same okiya. Later that night, Natasha and Maria rehash their geisha days by moonlight.
The next day, Roslin and Citrine put their rescue plan into action, and make provisions to break Ziggy out of jail. Back at home, Shion shares a moment with KOS-MOS.
to be continued...