The following was translated by the user NeoSmith from the xenotensei.com forums and lady-twi on livejournal. I’m just compiling everything for my personal pimping post.
Chapter 1
Episode I: Shion performs maintenance on the Woglinde’s Realians, and is approached by Virgil who we find is a DME addict and doesn’t like Realians very much. He calls them objects/equipment, and talks Shion down, telling her that she who is all for Realian rights holds a self-destruct code in the possible case that the Realians lose control - IE another Miltian Conflict type event. One of the ship’s Realians steps up to Virgil, telling him that yes, he is a Realian, manufactured and raised to do what he does (a Combat-type). But he takes pride in it and this pride he holds is of his own free will.
DS: This Realian’s name is Alex. We meet him first in KOS-MOS’s Simulation test - he was sent along with Virgil in his AGWS by the bridge to help take part in the tests along with Shion and KOS-MOS. Virgil still holds the hatred against him, deliberately shooting him when he’s within the line of fire of an enemy. Alex doesn’t die from the injury, but this is also interesting because of the irony this small addition poses later when KOS-MOS does the same to Virgil, killing him.
Chapter 2
Episode I: When Cherenkov enters the bridge, Captain Moriyama asks him if something’s wrong.
DS: Cherenkov has a strange dream about the recovery of the Zohar Emulator prior to this scene, and wakes up from the dream all flustered and sweating. This is why Moriyama questions him in Episode I.
Episode I: Shion performs maitenence on the Woglinde’s Realians.
DS: The Kirschwasser from Xenosaga: The Animation is among them.
Chapter 3
Episode I: The survivors escape in the pods, and KOS-MOS plants a tracer on the Gnosis that attacked and stole the Zohar Emulator.
DS: Shion breaks down crying in the escape pod after they launch, overwhelmed from what had happened. KOS-MOS is not shown planting a tracer on the Gnosis, as it had no real point in the original.
Shion’s first meeting with Kevin is unlocked somewhere toward the start of the game, I think. Read a translation of the whole extra scene here (edited out link).
Chapter 4
Episode I: KOS-MOS boards the Elsa. Shion and Allen follow suit. After these events, Ziggy and MOMO come across the Elsa by coincidence, after the rescue on Pleroma and ultimately wind up joining them.
DS: Ziggy and MOMO are on the Elsa before the arrival of KOS-MOS, Shion and Allen. Ziggy had already carried out the rescue mission on Pleroma. The Contact Subcommittee requested the Elsa aid Ziggy on his mission, making their being together less of a coincidence.
Episode I: KOS-MOS is put off by chaos’s sudden appearence on the bridge, having not detected the door to the bridge actually opening for him prior to his entrance.
DS: chaos calls KOS-MOS by her name before anybody gives it to him as well.
Episode I: Margulis and Pellegri discuss planet Ariadne.
DS: Pellegri asks herself what Jin would think of them if he were there.
Chapter 5
N/A
Chapter 6
Episode I: The cast meets up with Jr. and the Durandal. From the Elsa, Shion contacts her director about KOS-MOS. Jr. shows them the Emulators and Betty, and they arrive at the Kukai Foundation.
DS: Jr. tells MOMO that he sent the Elsa to aid Ziggy per request by Contact Subcommittee member Juli Mizrahi, and asks her a bit about Shion, Allen and KOS-MOS and how they wound up on the Elsa. Shion makes her call to the director from the Durandal instead of the Elsa.
DS: Margulis announces Plan 401, and talks about the Kukai Foundation’s recovery of the last Zohar Emulator. Pellegri is asked to bring Richard and Hermann in to join in the mission, which ties them into the storyline much more earlier on and gives them more of a reason for being there.
Episode I: Gaignun gifts Jr. with a gun he won at an auction.
DS: Gaignun is shown at the auction, bidding on the gun. He gets into a frantic bid war with a mysterious other person, but wins the gun in the end. We find out that this mysterious other bidder was Mary, who had the same goal as Gaignun in winning the gun (giving it to Jr.).
Episode I: Flashback: Cherenkov and his men rush the Vector lab. KOS-MOS’s archetype awakens and kills them all sans Cherenkov.
DS: There’s an extra flashback about Cherenkov, where he meets up with a contact who gives him something that ‘he trusts will work right’ in regards to securing the KOS-MOS archetype. He slowly positions his men in the Vector Lab and they attack, announcing themselves as U-TIC. He doesn’t seem to want to have to actually kill anybody so is happy when they listen to him. He activates KOS-MOS archetype, who as shown in the game, kills them all. Cherenkov also, interestingly, says “why is the skeleton moving? I only activated the AI.”
Chapter 7
We are introduced to a brand new character just featured in the DS game, a man named Pierre Ruryk who is part of Dmitri Yuriev’s Salvator faction.
Episode I: The Durandal/Kukai Foundation are accused of treason and the destruction of the Woglinde.
DS: Ruryk appears in favor of the Foundation, but Jr. gets strange vibes off of him. Gaignun wonders if Ruryk is aware of his and Jr.'s true identities, given his position as a Salvator.
DS: The Patriarch Sergius appears early on here, as opposed to much later in Episode II. He is against the Kukai Foundation and explains that they destroyed the Woglinde and took the Zohar Emulator that was stored on board. He adds that the Zohar belongs to his people, and even though management for the Emulators are under the jurisdiction of Second Miltia, that they should get that power over them. Ruryk and Juli try their best to defend the Foundation.
Richard and Hermann are disguised as Federation soldiers and run into the team when they escape and head to the Elsa to find KOS-MOS. Richard is super violent, but Hermann listens to his orders either way, promising to protect him.
Chapter 8
Episode I: In the Encephalon, you run across the game’s mascot, called Bunnie. As an extra minigame of sorts, you can get into his house by using carrot-juice to lure him out.
DS: Shion, chaos and Allen encounter Bunnie in the forest, and Allen tries to catch him. Upon doing this, Allen sees Bunnie’s second face (which if you look at Bunnie, its normal face is… normal! while its second one is dark and creepy and on the other side of his head) which shrinks him. When they try to get Allen back to normal, Bunnie tries to do the same thing to Shion, but Allen jumps in front of her, which turns him back to normal.
Episode I: The cast leaves KOS-MOS’s subconscious.
DS: When the cast leaves KOS-MOS’s subconscious, they find that the Salvators, led by Ruryk, have gathered an amarda around the Kukai Foundation to put pressure on those who are trying to accuse them and Second Miltia of their crimes. Government members are surprised to see that the Salvator Faction has an entire army.
Episode I: The Kukai Foundation and Second Miltia are cleared of their charges.
DS: When the Kukai Foundation and Second Miltia are cleared of their charges, Ruryk speaks to Gaignun through video and Jr. asks him why he did what he did for them. Ruryk explains that he has sympathy for the Kukai Foundation and Gaignun, and he appreciates what they do. Ruryk, up until now, had addressed Gaignun as “Representative Gaignun”, but now calls him “Master Gaignun” which catches Gaignun by surprise.
Chapter 9
Episode I: MOMO disappears and we find it was Albedo who kidnapped her in the midst of the panic in the Kukai Foundation.
DS: We see the Simeon actually enter the Kukai Foundation.
Episode I: Albedo scares the crap out of MOMO by cutting off his own arm, and then his own head only to grow both back.
DS: Instead of using a knife, Albedo shoots his own head off with a gun in front of MOMO. Possibly a change to better reflect younger Albedo’s identical actions in Episode II.
Chapter 10
Episode I/Animation: The Kirshwasser follows Albedo. The Kirshwassers in general follow him out of a want to feel as if they’re needed. They also see something in him, despite his actions in killing and torturing them all.
DS: When the Blue Testament arrives and Albedo leaves, the Kirshwasser stays behind. The Blue Testament telepathically tells her that if she doesn’t go with him, he would kill her. So she panics and follows him. Albedo tells her that there was something else she could do for him to be useful, regarding his E.S. Simeon and a Vessel of Anima. The Blue Testament falters because of the change of plan that results from Albedo’s actions.
We also get a flashback of Nigredo/Albedo fighting in Miltia 14 years ago. Nigredo had come to carry out his role as executioner to a contaminated Albedo. After their fight, it was never explained deeply how Albedo was rescued. Sellers had left the Kirschwasser on the Song of Nephilim, where she found him, staying by his side since.
Episode I/Animation: The final confrontation takes place in Proto Merkabah. Prior, in the song of Nephilim, the battle with the Simeon happened before the Blue Testament’s first appearence, meaning the Simeon doesn’t show up in Proto Merkabah.
DS: The Simeon is summoned in Proto Merkabah, and the Kirschwasser says goodbye to Shion, who recognizes her as the one from the Woglinde. The Vessel of Anima in the Simeon absorbs her, as she willingly gives herself to it out of her want to be useful to Albedo. With the Simeon as strong as it is, the cast can’t take it by themselves. The E.S. Asher appears, piloted by Canaan (and apparently sent by Helmer) to fight with Simeon. The Vessels of Anima within the two E.S. resonate strangely which result in both E.S. becoming paralyzed. Canaan tells Jr. and the others to get away and take care of Proto Merkabah’s reactor.
Chapter 11
Episode II: The Elsa’s crew arrives on Second Miltia. After parting ways, Richard and Hermann, in the Joseph and Gad chase Ziggy, MOMO, Jr. and chaos as they head to the U.M.N. Control Center to analyze MOMO.
DS: Margulis informs Richard and Hermann about the Asher and Simeon’s strange resonation, and talks to them about these special E.S. units that possess Vessels of Anima. Richard and Hermann possess “the factor”, among thousands of Inquisitors, and Margulis entrusts them with the Gad and Joseph, which are not completely restored yet. When Pellegri seems concerned with this, Margulis says that he just cares about the results, and that if the E.S. or the pilots are destroyed, they can always just recover the Vessels of Anima and restore them elsewhere. When Pellegri hears this, she gets more concerned as she had just acquired her E.S. Issachar, but Margulis tells her she’s different, and doesn’t fall under that “throwaway” category.
Shion thinks about the Kirshwasser, when her thoughts are cut off by an alarm and an announcement saying that two E.S. units have broken through Second Miltia’s defense line. Jin, at his home on Miltia, deduces that “the Colonel” is making his move upon hearing this. Jr., however, wonders if it’s just the Asher and the Simeon still dueling. He’s proven wrong when Canaan approaches them on foot, and injured, and informs them that the two E.S. units are probably U-TIC. When Jr. introduces Canaan to the group, Ziggy gets a strange feeling about him (throwback to his Pied Piper story).
Canaan explains that when Proto Merkabah penetrated the atmosphere, he separated from the Simeon and fell into the sea. The government had recovered the Asher, and in order to use it against the two new E.S., he needed chaos’s power to restore Asher.
When they head toward the Asher to do this, Richard and Hermann catch up with them, and chaos recognizes the E.S.s right away. Richard and Hermann demand that they hand MOMO over, and KOS-MOS and Shion move in to attack to buy the others enough time. When the group reaches the Asher, chaos wonders if he should restore it and wonder if this is all the work of “that man”. Suddenly, MOMO detects something as a Vector craft crashes into the scene, boarded by Miyuki and the E.S. Zebulun - the E.S. was offered by Wilhelm to Helmer in order to help them.
Richard and Hermann retreat when they realize two E.S.s are heading for them. KOS-MOS’s frame is close to destroyed, but with Miyuki’s arrival, she tells Shion they can take her to Second Division to give her her new combat frame. chaos wonders if their close call was also part of “that man”'s script.
Chapter 12
Episode II: KOS-MOS is taken to the Second Division, and given to new hands, much to Shion’s upset.
DS: After Shion leaves the Division, still upset having to had given up KOS-MOS, she wonders to Allen if they were contacted about the unauthorized dive into KOS-MOS’s encephalon. Allen tells her that they won’t be blamed for it, because it was something necessary to clear the Kukai Foundation’s name. Shion finds this strange, wondering if somebody in Vector had pulled strings for them.
DS: Here we see Sellers getting into the picture a little more. Talking to Ormus’s leader about Pleroma’s destruction. Margulis is also present, saying that Richard and Hermann failed on Second Miltia, but they still had other ideas for opening a route to Old Miltia. The mysterious Ormus leader tells Sellers to assist Margulis. After this, when Margulis is alone, he wonders how the “old man” will react when he finds out what they are doing (most likely Patriarch Sergius), and that he doesn’t trust Sellers, adding that if he becomes a problem, he would kill him in an instant.
DS: Margulis reprimands Albedo for losing Proto Merkabah with no accomplishments, but Albedo just laughs at and mocks him, saying that he’ll have results soon enough. Margulis tells him about a new E.S. on Second Miltia, and suspects that the Salvators are involved somehow. He wonders why he would have a reason to fear Dmitri Yuriev when Albedo asks him if he did, and Albedo adds that “the executioner” had killed Yuriev, but nobody should expect that he would remain dead.
Episode II: Jin and Shion meet again - with chaos and Jr. in tow. After their small family arguments and chaos and Jin’s talk in the garden, the next day Shion heads out.
DS: When Shion leaves, she runs into Allen, who wants to check out her hometown. Shion says they should spend some time together and takes him to a park, where the Dammerung is in the sky. She says that when she doesn’t feel well, she comes here to look at the stars. Allen asks her what happened to make her want to come here now, and reflecting for a moment, she says that nothing bad actually happened.
Allen proceeds to tell her a little about his own family. The entiretly of this extra scene is translated here.
Allen’s first meeting with Shion is also fully translated here.
Chapter 13
N/A
Chapter 14
The following has been changed quite a bit from the game, and a whole new arc of the story has been added in Chapter 15 which connects to this. Also, obviously since these are flashbacks with present characters watching them, “Jr.” and “Rubedo” will be differentiated. As will “Gaignun” and “Nigredo,” as well as “present Albedo” and “young Albedo”
Episode II: The group dives into MOMO’s subconscious, and here we see the past of the U.R.T.V.s and Sakura - the girl MOMO was modeled after. It ends in Albedo’s trap which ultimately leaves him in acquiring the Y-Data from MOMO.
DS: Jr. gets anxious as they move on in the story, knowing that they’re going to relive memories that he doesn’t want to remember. He collapses when Sakura’s phantom in the dive walks through him.
When Rubedo gets his harmonica, young Albedo starts showing his strange behavior when he mentions U-DO. He thinks they were created to access it, and wonders how it would feel to come into contact with it, saying it would be great and they would have so many possibilities to evolve thanks to it. Rubedo punches him and lectures him about it, and this is also where young Citrine first appears. She seems honored to meet Nigredo, and simply leaves when she tells them her U.R.T.V. number.
Episode II: Young Albedo talks about his dislike for the standard U.R.T.V. units. Rubedo sticks up for them, but the standards still look upon Rubedo with hatred, calling him a monster as their leader.
DS: The standard units actually gang up on Rubedo and begin physically hurting him. When young Albedo sees this, he rushes in and attacks one, beating and beating him and demanding that he apologizes to Rubedo. Despite the standard’s previous actions of hurting him, Rubedo begs young Albedo to stop and Nigredo jumps in to separate them.
Episode II: First, the U.R.T.V. training in the Summer-Domain ends in some of the units getting contaminated. THEN comes the Winter-Domain, in which they go with Sakura to the beach to try and cure her illness.
DS: The U.R.T.V.s meet up with Sakura, and they’re told the reason for diving - that if their mission was a success and they managed to clear Sakura’s mind of U-DO’s contamination, then she would be able to talk and function in the real world again. Rubedo loves the idea of going to the beach with Sakura, even if it’s still in her subconscious domain, and heads there with her holding hands, running ahead of the others. Young Albedo talks to Nigredo - saying Rubedo should be more focused on the mission, but Nigredo says it’s fine and moves to catch up with them. Alone, young Albedo realizes that other than his mission and Rubedo, he had nothing of importance.
At the beach, Sakura asks Rubedo if he remembers his promise, and he says he can’t forget it, and promises again to free Sakura of her illness. This is when U-DO’s waves appear, attacking Rubedo. The rest of the U.R.T.V.s arrive, and Rubedo orders them to form their link, but it’s too late as some of them have already been possessed by the waves. In the midst of it all, Citrine jumps in to help Nigredo, and he wonders why she would help him in particular. Rubedo, unable to move, tells young Albedo to go save Sakura, and he heads off running.
After they subdue the units, Rubedo and Nigredo run to find young Albedo and Sakura. Sakura is dead on the beach, and young Albedo is at her side, mumbling U-DO’s name. Jr., who with the group had watched the entire flashback, silently promises to MOMO that he would never let something like this happen again.
Chapter 15
This is a brand new added chapter to the storyline, still taking place in the subconscious dive, only a couple of months or so later. So Yuriev, Helmer, etc. are all from the time of the dive, 14 years ago.
Dmitri Yuriev and Helmer talk about Miltia - people responsible for the coup d’etat refuse to return Joachim Mizrahi to the Miltian government. These people responsible seem to be military folk of the former Miltian government, and Yuriev suspects the Immigrant fleet to be involved. Yuriev claims to forsee the outcome of the descent operations, and since the second descent to Old Miltia failed, he wants to sent the U.R.T.V.s in. Helmer claims that he’s merely an ex-politician and can’t support this demand, but Yuriev simply says he’ll act on his own judgement. Shion realizes this is the last stage of the Zoar Incident - the Miltian Conflict.
Jr. explains that after the death of Sakura Mizrahi, Joachim started extreme research. When he had obtained the results, this caused part of the government to begin the coup about a month ago. The Federation, refusing to accept this new government, launched a bunch of military operations.
chaos speaks to Nephilim, asking her if she’s “going to interfere”. She answers, saying that in this time, she already intervened, so she was going to sit back and watch things unwrap - chaos finds this a good decision.
Back outside of MOMO’s subconscious dive, Shelley and Gaignun wait for them to return. Gaignun hears a voice in his head that tells him to “go to the land of awakening, for the time of his awakening has finally arrived”. Once he snaps out of his strange trance, he asks Shelley about Jr. and the gang’s progress. After she tells him about it, he says that he can’t keep standing there and waiting, and that he has a card to play on Fifth Jerusalem. Shelley has no idea what he is talking about or why he wants to go there, but he assures her to have faith in him. When Shelley leaves, Gaignun asks himself why he wants to go there, and what he wants to do there. This is better foreshadowing to Dmitri’s rebirth.
Back in the subconscious dive, they find themselves on Proto Merkabah. It and they are still on Miltia, and Jr. realizes that the Gnosis are soon going to appear. The U.R.T.V.s are already on Miltia, and getting ready to accomplish their alleged mission - to destroy U-DO. Led by Rubedo, they head off.
They run into another U.R.T.V. team led by young Citrine, who collapses from a wound she obtains from protecting Nigredo from a soldier. Rubedo gets concerned about Nigredo, whose concentration is faltering out of his strangely deep concern for Citrine. When Rubedo asks Nigredo what him and Yuriev talked about before the mission, Nigredo jumps, obviously bothered somehow by his question. Young Albedo tells them to concentrate, and assures Rubedo that they’ll be fine despite the dwindling number of the U.R.T.V.s thus far. His confidence worries Rubedo, so he decides to form their mental link to go up against U-DO.
Nigredo doesn’t understand why he doesn’t react to or feel anything. He wonders if it could be because he is the “executioner”. Infected U.R.T.V.s appear and rush the group, and after they are dealt with, the events from the flashbacks in Xenosaga II with the breaking of the mental link and Albedo’s contamination occur. The ground begins to rumble, and Jr. orders everyone to hold hands so they could transport somewhere else.
When they wake up, they’re in a ruined city, and Jr. realizes this as the middle of Miltia’s third descent operation. Ziggy wonders why Albedo would make them all relive Jr.'s past like this, which infuriates Jr. This makes Ziggy figure that pushing Jr. over the edge is also part of Albedo’s plan in bringing them all there.
They see Nigredo’s body on the ground, and Jr. realizes that they need to save the civilians from the contaminated U.R.T.V.s – who were killed originally by Nigredo, shown in Episode I’s flashbacks. This change is part of Albedo’s trap in the subconscious, to make Jr. and the team take the acions, and come and confront him on the Song of Nephilim in Nigredo’s place. Originally, Nigredo and young Albedo faced off there 14 years ago, but as this is Albedo’s trap in the subconscious domain, he makes those who dived and are reliving it follow Nigredo’s footsteps to wind up in the same place to meet present-Albedo-- he’s trying to mirror the events of the past basically, only with Jr. and the team and himself. When they arrive, young Albedo attacks Rubedo and beats him to the ground and then absorbs the bodies of the U.R.T.V.s around him. He’s thrilled to be in front of U-DO, and yells that he was the one who killed Sakura.
This pushes Jr. over the edge. Sakura with MOMO as an intermediary appears to try and calm him down. Then, present-Albedo breaks into the Encephalon, thrilled that Jr.'s lost control. About to push him even further, he’s stopped by MOMO, who can’t take any more, and begins to leak the Y-Data. They realize this was his plan all along, the leaking of the Y-Data is taking its toll badly on MOMO, she risks losing her consciousness. Sakura jumps in, and pauses at Jr., saying that she’s always been with him, that she’s always had so many things she wanted to tell him, but there was something she must do.
After saying goodbye to Jr., she appears in front of MOMO, and explains that she always lived inside of Jr., but could not express herself. She thanks MOMO, because in her subconscious she could finally talk a bit to Jr., and in return she would perform the Y-Data’s transfer through MOMO’s inner-world. She takes MOMO’s place and disappears during the transfer. MOMO regains her consciousness in the real world, but the Y-Data is gone.
The Kirschwasser’s substory is unlocked here, too. Read a translation of this extra scene here.
Episode II: Albedo opens the seal to Old Miltia
DS: When Albedo opens the seal to Old Miltia, this pings Gaignun, who calls Albedo an “indignant son”. Gaignun pauses, realizing what he just said and wondering why he said it. He recalls a conversation with Citrine, where she explains to him their similarities in their mission regarding Jr. - the Red Dragon (this scene was in Episode II) After this, he thinks of his meeting with Yuriev before the Miltian Conflict, in which he kills Yuriev, this was also in Episode II.
Episode II: Yuriev takes over Gaignun’s body.
DS: This is when Yuriev starts to take control of Gaignun’s body. After he’s taken over his body, Citrine contacts him telepathically, and he asks her to give him all the news of the current situation. Once she briefs him, he orders her to prepare the Salvators’ military, because the race is about to begin. When Gaignun regains his body, he’s still telepathically linked with Citrine, asking her things like who she is. She responds with “your spirit hasn’t expired yet?” and then goes on to say that they’re both serving their father, so should be proud. “Who… am I?” “You’re Dmitri Yuriev. My father, my most beloved.”
On the Durandal, MOMO tells Jr. what happened to Sakura, and he thanks her for what she’s done, promising MOMO that he’d look after her.
Chapter 16
Margulis talks to the Patriarch Sergius about the sudden appearance of Gnosis. They react to the Zohar that sleeps on Old Miltia, therefore the path has been opened. Sergius still feels that the Zohar belongs to Ormus, so they must head toward Old Miltia to obtain it. At the same time he worries about no longer having contact with their mother planet, but Margulis says that it’s probably because of the Gnosis and that nothing could be done. Their forces are deployed to defend the planet, but at the same time it means they will be late in researching the Zohar. But thanks to Mizrahi’s work, Margulis muses, they won’t have too much trouble catching up with that.
Episode II: After Albedo opens the seal, we simply move to Shion on the Dammerung.
DS: Shion prepares to leave Jin’s house, saying that after they attempt to activate KOS-MOS, she’ll return to the Dammerung. She stops by to see MOMO, and Shion remembers that she promised MOMO they would visit Second Miltia together. So keeping her promise, they go to do that, but as they do, Jr. gets an “urgent” call from the Durandal–namely, an angry Mary who wants him to join her video club. She had created a funny Japanese video and sends that to him instead of the message. Jr. asks her about it, but she takes it the wrong way and accuses him of dishonoring the club. They’re cut off by MOMO who detects Gnosis about to gate out in the middle of the city. Shion tries to contact Allen to see if KOS-MOS is operational while Jr. tries to contact the Durandal to launch A.G.W.S., but can’t get through to them. They try to call their E.S., but something else appears (unclear) that the Gnosis attack instead.
Ruryk tells Yuriev about the plans to depart to Miltia. Yuriev is not quite ready to disembark themselves yet, so sends Ruryk and the Salvator Fleet instead. Ryryk is a little hesitant about going, but Citrine compliments him and ge goes. After he leaves, Gaignun takes over Yuriev’s body, sees Citrine and starts to panic. Citrine simply tells him that this was his punishment for murdering Yuriev in the first place, and that he wasn’t like Jr. and Albedo, he was always meant to serve his father.
While the Gnosis attack Second Miltia and Shion & co. hold them off, they move to stop the lone Gnosis responsible for the communication jams. KOS-MOS wakes up by herself here, and leaves Allen and the Second Division behind to go and rescue her (which happens in Episode II, but much differently). They’re all surprised at her new frame (version 2), but she simply tells them that that’s all that’s changed about her. chaos thinks that her “soul” must still be there as well. They find the Gnosis causing them the big problem and defeat it, restoring the communications.
Helmer thanks them, but sends them on another mission with the E.S. to stop the Gnosis responsible for all of the others appearing. Helmer also asks Jr. if he knew why Gaignun suddenly left for Fifth Jerusalem, but Jr. doesn’t know, which worries him. After the battle, Jr. loves having three E.S. on their side, and Shion feels nostalgia over piloting the Dinah. Not quite from Kevin developing it, though, more of a distant past nostalgia.
Chapter 17
chaos and Wilhelm have a conversation. Wilhelm tells chaos it’s been a long time, and he’s happy to hear his voice. He then goes on to ask him about regarding the events thus far as an observer/guardian, noting that he was close to all of the people he entrusted an E.S. to and yet never contacted him. chaos says that Wilhelm’s interventions are brutal, and that in the past the E.S. have caused nothing but tragedy due to being aligned with the Vessels of Anima. Wilhlem says that the Vessels are from chaos’ origin, which was why he was so upset.
Margulis and Sergius talk about their advancement and the movement of the Second Miltian government. Pellegri worries after Albedo’s lack of communication with them, and they assume that Albedo might have completely cut off ties to go solo.
Episode II: Shion and Allen arrive on the Dammerung, where Shion has her dreams about Feb/sees Nephilim.
DS: Shion and Allen arrive on the Dammerung. Shion is a little sad that she had to part with the others, who were departing for Old Miltia to see what Albedo is after. She gets her transfer notice to the the Third Division on Fifth Jerusalem, but after seeing Nephilim and Febronia appearing in her dreams, she’s torn about going.
On the Durandal, Gaignun apologizes for not contacting them sooner (he tried, but it was durring the Gnosis attack where communications were down). Jr. asks him about why exactly he’s in Fifth Jerusalem, and Gaignun explains he was doing some investigation on the Salvators, since they more than likely have data on the U.R.T.V.s and have prepared a fleet to launch to Old Miltia. In response, Jr. goes to meet with Canaan, and “Gaignun” thinks to himself that Rubedo really is the easiest son to manipulate.
Episode II: After Shion’s dreams/visions, she steals the Dinah from the Dammerung with Allen, is saved by KOS-MOS and picked up by the Elsa.
DS: Jr. and the rest prepare to launch on the Elsa to head to Old Miltia. As they’re about to launch, chaos announces that he feels the interference of a Vessel of Anima, and the crew is ready to fight. But MOMO identifies the E.S. as the Dinah and Shion/KOS-MOS. Jr. is happy, saying they have the power of 100 men now. Allen announces he’s there too, and Jr. changes that to the power of a 100 and a half men. They explain they got an order from Vector to participate in the Kukai Foundation’s mission to recover the Zohar. chaos thinks to himself that he’ll have to make a decision soon.
Yuriev contacts Helmer, who is shocked to hear his voice. He tells him that his Salvator fleet has also been sent toward Old Miltia for the Zohar, and somehow knows of the Kukai Foundation’s plans. He makes it clear to Helmer that he wants to reach the group with his fleet, and that he wants one of Helmer’s best advisors since the Salvators don’t know Old Miltia very well. Helmer chooses Jin, on account of his hope that they’ll finally be able to examine the data Canaan holds.
Episode II: The Elsa must pass through the Ormus Stronghold in order to reach Old Miltia.
DS: MOMO detects a huge gate-out, fleet-sized so there is impending battle over the Zohar. Since they’re not sure who these adversaries are, they launch in their E.S. to protect the Elsa as they break through. They fight an A.M.W.S. of unknown origin, and Jr. realizes it’s the Immigrant Fleet due to the technology they’re using (which is the same they used 100 years ago), but this seems off because if ths organization was as peaceful as they claimed to be, why would they use such powerful energy? When they confirm their enemys’ identities, Albedo decides to intervene.
Ruryk and Jin are with the Salvator Fleet, and deduce that Albedo and the Immigration fleer and among the fighting. The Immigrant is using a defense field that reacts to the waves of the Zohar, which causes Ruryk to decide to use their “new” weapon, pod U.R.T.V.s fabricated from the ones sent to Old Miltia.
A huge Ormus mobile weapon gates out and takes these U.R.T.V.s out. Ruryk makes some bad choices (as noted by Jin) and the Salvator Fleet is almost wiped out in a single blow. Ziggy recognizes the huge Ormus weapon,and they all wonder how much links U-TIC has with this. chaos senses the Simeon , and Jr. launches to fight it in order to clear a path for the Elsa, by entering the weapon. They’re attacked by other A.M.W.S. along the way, but Jin appears and saves them (with his katana). Shion and Jr. are surprised that Jin an chaos have known each other for a long time. He tells Jr. about these pod U.R.T.V.s-- apparently the … pods? are too small to hold a whole body so they only contain pieces. The Salvators continued their research on the U.R.T.V.s and used their cerebrum/waves to break the waves of the Zohar and thus ruin the Immigrant Fleet’s power source.
They find Albedo, who is fighting Richard and Hermann and forcing them to retreat. Jr. tries to ask him why he’s there, but Albedo ignores him and sends mass energy into the generator, causing it to lose control. He then tells Jr. that if he wants to really know, he’ll have to survive this. Hermann, still there with Richard, suggests they escape, but Richard wants to stay and fight Jr. and the others. They battle, and after it’s over chaos asks them not to use the Vessels of Anima, and Richard and Hermann escape. The party evacuates before the generator explodes.
Chapter 18
Episode II: The crew lands on Old Miltia, make their way through Labyrinthos.
DS: When they arrive at Old Miltia together, Jr. realizes Albedo’s plan - to start a battle between the Salvators and the Immigrant Fleet to buy himself time to get to the Zohar first. Jr. also thinks he understands Albedo’s true goal since the dive into Sakura’s domain.
The Testaments are watching these events, and considering there are three of them, and three teams of ES (Shion & co, Richard and Hermann, Albedo), they decide to split up to encounter them. Red wants to go after Shion’s group, but Blue opposes this, saying that he also had something to settle with them (Blue also talked about how he felt seeing Old Miltia again). So Blue goes after Shion’s team, Red goes after Albedo (“the key for calling Abel’s Ark”) and Black takes Richard and Hermann, who he calls for good-for-nothings. Red warns them to be careful about coming into contact with the E.S. if Yeshua is near.
Shion flashbacks a lot more to her past here, Febronia getting killed for someone. The Blue Testament attacks, destroying the place/grave Shion’s parents’ bodies were. This causes Shion to panic and freak out as they try to get to a shelter when guards start to appear. In her anger, Shion snaps at MOMO and calls her “Realian” as more of her memories flow into her mind-- her father protecting her from the Asura series. She yells that Realians are the cause of her parents’ and Feb’s deaths so she doesn’t want to be touched by one of them. The Blue Testament tries to cause them more turmoil by explaining this is Shion’s true nature-- but chaos argues with him, and gets told that he, who is not a human either, shouldn’t be speaking of human nature. chaos notes that The Blue Testament was also a humam before becoming what he is now, and that he wears his mask to hide that part of him. This causes the Blue Testament to attack them. Shion apologizes to MOMO after that, and the Blue Testament says she just tried to throw away her past, trying to hide her hate for Realians by trying to work with and help them. MOMO sees this differently, though-- as perhaps trying to face this thing you hate in order to try to change. After the Blue Testament leaves to wait for them in the depths of Labyrinthos, Shion tells Jin that they should visit their parents’ graves after this.
Albedo feels that Jr. made it to Miltia. The Red Testament appears and Albedo notices right away that their goal is to buy time and distract him. Despite this, Albedo is excited to see how he measures up. Richard and Hermann come across the Black Testament, who easily provokes Richard, thus making them fall into their plan to make them waste their time.
During Canaan’s data analysis, Margulis appears and attacks. The data expands a bit on the information revealed in Episode II, namely, doesn’t completely clear Joachim Mizrahi’s name. Immigrant Fleet came from Lost Jerusalem, took the Zohar with them, Mizrahi being from Abraxis meant there was a strong chance he was part of them. Fearing a repeat of the Miltian incident, Shion and co. move on to find it.
When Shion sees Cecily and Cathe, she remembers playing with them as kids and growing flowers for Feb, as opposed to learning this all in Episode III. The Blue Testament keeps instigating Shion when they realize they have to kill them, saying that it should be easy to do for her, who detests Realians so much. When they destroy them and by proxy, Shion has a moment of relief/pleasure, but the Blue Testament is mistaken when he thinks it’s because of her “hatred.” She wanted to relieve Febronia, and upon hearing Feb’s name the Blue Testament looks disturbed, seeing a vision of her.
Jin and Pellegri meet after the activation of Proto Omega. She doesn’t understand why Jin left them, and they battle. Afterward, Jin tells her to contact Margulis to tell him that he has no doubt anymore. After Miltia is destroyed, Shion wonders why Nephilim wanted her to go there, since all she did was suffer.
Chapter 19
Pellegri has some inner thoughts about first betraying the Federation, and now doing the same to Ormus. Margulis ignores an order from Sergius to launch the ES to face the Salvator Fleet. When Margulis leaves, Sergius fires Proto Omega on the Fleet, destroying it. It’s also revealed here in a convo between Albedo and the Red Testament that their actual goal wasn’t to stop them from getting to the Zohar, but to stall them while Sergius gets to Proto Omega. The Red Testament offers a deal to Albedo, help them with something, and in return they’ll give him anything he wants.
Episode II: Yuriev contacts Jr. on the Elsa. After he disconnects, tracing the location of his call is said to be difficult.
DS: When Jr. asks Hammer to trace it and Hammer says that it could take a while, Jr. mentions them a bonus if they find it. So Matthews, excited by this, tells Hammer to drop his navigating for this new job.
Episode II: After the destruction of Miltia, Shion has a long conversation with Jin.
DS: After this conversation with Jin, Shion runs into Ziggy and asks about him and his family. Ziggy tells her that he was an officer on Abraxis/Michtam. That he met Sharron, and her and her son became his family. Shion feels nervous about asking him any more than that, so doesn’t. She also runs into chaos, who asks her how piloting her E.S. is. She tells him that there were no problems, and this worries chaos, who thinks about how everyone is adapting so easily to the E.S. Jr. also worries a little about his father being back, determined to act how he wants to, rather than what his father tries to order him to do.
Episode II: The crew meets up with Albedo, who gets turned into “particles” from an attack by Sergius and Proto Omega. The team fights the two.
DS: When Jr. breathes in some of Albedo’s particles, he seems to understand what he was doing. Him and Shion get enrages, and the Zohar seems to reaction to their emotions. Sergius questions if the two of them are connected to the people of the Zohar, and chaos detects resonance with the Vessels of Anima, fearing that something that has already happened will repeat itself. Sakura and Feb communicate with Jr. and Shion to calm them. After the battle and aftermath of it, KOS-MOS activates her Tertiary Weapons System,and Shion remembers the future Nephilim showed them in Episode I, fearing that it was coming true.
Chapter 20
Somebody tries to contact Albedo. Despite being particles, Albedo still has his consciousness. Whoever is contacting him wants to lend him power because they need him, and want him to contact U-DO. Albedo refuses, but he’s forced into it and contacts U-DO.
On the Elsa, Shion demands to know why KOS-MOS did what she did, but she simply explains that she did it to stop the anomaly, and can’t give away who programmed her to protect Shion. MOMO confirms that KOS-MOS’s actions did stop the anomaly for the time being. But if they don’t stop it soon, it’ll spread through the universe and “a new world will be born.”
Albedo contacts Jr. much like in Episode II before their final battle. He tells Jr. he wants to create a new world, and Jr. knows that it isn’t what Albedo really wants. He wonders why Albedo knew so much 14 years ago but never said anything. Jr. goes to visit Ziggy after hearing Juli sent him new parts over the U.M.N. for repair. Ziggy explains his past to Jr., and Jr. leaves to go after Albedo. But the team joins him, telling him they have reasons to go too-- to stop the anomaly. When Jr. tries to talk them into not coming with him, MOMO slaps him. Jr. explains after that he has to fight Albedo, and doesn’t want them to see this other side of him. MOMO says that regardless of any of that, they want to go with and support him.
Episode II: Jr. goes into the anomaly to confront and defeat Albedo.
DS: The whole team goes into the anomaly. They still see Albedo’s taunting to Jr. from Episode II in the form of little Albedo telling Jr. is he’d let his friends die like he did 14 years ago, and telling him “searching” MOMO in Episode I on the Song of Nephilim was pleasurable and if Jr. did it he’d feel the same way. When they get close, Shion wants to stop Jr. from fighting Albedo, but Jr. tells her they were here to make Albedo disappear, not to reconcile. Albedo realizes that after Jr. breathed in some of his particles he understood everything, including what really happened the day Sakura died. Which is as follows, tranlsated by jinxhaas on gamefaqs.com:
Little Albedo: !? What’s this?
U-Do: …
Little Albedo: You… were looking… for me? … No.. I was looking [for you].
U-Do: …
(Albedo touches the spherical object)
Little Albedo: …yes, that’s it… I was born for the sake of accessing you.
Sakura: No, don’t! Albedo!
(Sakura throws Albedo aside, touching the sphere. The object disappears and Sakura collapses.)
Little Albedo: Y- You… why… for Rubedo’s sake? If it’s for Rubedo, you would go that far?
Sakura: You’re wrong… it was for your sake…
Little Albedo: What are you saying?! I was going to be e- evolved by U-Do… Right before my eyes, the door to a higher-domain was opening… Why-- Why did you interfere?!
Sakura: Your… true wish… is not like that.
Little Albedo: What, d- do y- .. you know?!
Sakura: You always… with Rubedo…
Little Albedo: H- hey.. why are you quiet all of a sudden? Quick, you gotta regenerate… Rubedo will be here soon! If Rubedo sees you like this… get up… get up, pleeeaseeeeee!
The rest takes place as it does in Episode II.
Episode II: After the battle with Jr. and Albedo, chaos confronts Wilhelm about not hesitating anymore. Abel’s Ark appears. Ending/credits, Jr. gets a new dog.
DS: When Jr. gets the new dog, Alby, Gaignun appears, surprising them all. He threatens to take away Jr.'s gun collection if he keeps doing durpy things like that. Jr. thinks about what Albedo warned him about with Gaignun, especially since Hammer’s trace from Yuriev’s call said it came from the Durandal.