Plot summary of Xenogears - Part 3

The third part of Xenogears, consisting of chapters 29 to 39, is set in Aquvy and focuses primarily on the Ethos organisation and its affairs.

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Chapter 29: Adrift at Sea

Elly and Fei find themselves on a small raft with a few days' worth of food; their Gears are secure but inaccessible below the raft. Fei feels that the others are okay and goes to catch some fish. Meanwhile, Citan, Rico, and Hammer awaken on the Yggdrasil. They speak with Bart, who half-heartedly apologises for shooting down their ship. Rico is unimpressed and attacks Bart.

After Fei catches a fish, Elly notices and points out Shevat flying overhead, and Fei recognises it from the Dazil desert. Bart, meanwhile, goes and apologises properly to Citan (who admonishes him for jumping the gun, and notifies Bart that the crest on the new Yggdrasil is that of Shevat) and to Rico (who has gotten the anger out of his system already). Rico agrees to join Bart's crew. Fei and Elly conversate about their places in the world, and Elly decides to leave the Gebler Special Forces and stay with Fei.

Chapter 30: Men of the Sea

The next morning, Fei wakes up Elly, as he sees a large salvaging vessel known as the Thames on the horizon. They are rescued, as ordered by the vessel's captain. Fei and Elly's Gears have been taken to the Thames' supply dock to be repaired due to water damage, and they go to the bridge to meet with the Thames' captain. The captain proclaims himself a "man of the sea", and his greatness leaves Fei and Elly speechless. The captain says that the Thames does salvaging for various clients, including an upcoming large-scale salvaging job for the Ethos.

Meanwhile in a Gear deep underwater, Dominia, and another member of the Elements named Kelvena, detects a signal from the Yggdrasil. Dominia chooses to attack the Yggdrasil, despite Kelvena objecting. Suddenly, Fei and Elly feel shaking aboard the Thames, and outside, they see the Yggdrasil being attacked.

With the repairs on Fei and Elly's Gears being completed, Fei and Elly go underwater to help assist Bart in the fight. Dominia is surprised to see Elly leaving behind the Elements, and Fei, Elly, and Bart engage in battle with her. Dominia manages to capture Elly, but Kelvena convinces Dominia to retreat. The Yggdrasil crew decides to head to the Thames to perform repairs, as well as consider what to do regarding Elly's capture.

Chapter 31: Friends Again

Bart and the Thames' captain meet for the first time and begin to have a "man-to-man talk", when suddenly Margie enters the room, interrupting the moment. She also immediately embarrasses Bart by revealing to Fei that Bart was the one who shot down the Goliath. However, the Thames' captain finds this entertaining and shows Bart to the beer hall.

Aboard a Solaris airship, Elly gets attacked by Dominia for betraying them. Before the fight escalates, Miang stops Dominia and scolds her for attacking Elly and the Yggdrasil, and not following orders. As Dominia argues her position, Miang's eyes flash, leaving Dominia stunned and bewildered. Miang takes Elly to the airship's medbay and tells her that she needs to recover from her fatigue. Miang's eyes flash again and she leaves Elly in the medbay.

Miang shows Ramsus the report of the battle between the Haishao and the party, and Ramsus is surprised by something in the report, leading him to change the airship's course to the Thames promptly. However, Miang says that they should eliminate the Yggdrasil first and that she's already made the arrangements to sabotage it. Elly flies away from the airship in her Gear.

Back on the Thames, Fei finds Bart and the Thames' captain bonding over how they're both strong and "men of the sea", but they are interrupted by Elly returning to the ship.

Chapter 32: Betrayal

Elly says she will rest in the Yggdrasil and leaves, but Bart still has qualms about Elly, as he's afraid of her connections to Gebler. However, he ultimately leaves it up to Fei to decide whether or not to befriend her. Elly heads to the Yggdrasil's engine room and sabotages the engine, but Fei and Bart catch her in the act. Elly falls unconscious, and Bart says that he knew she shouldn't be trusted. Citan walks in and stops the sabotage attempt, and he says that Elly was under strong hypnosis and that he followed her here when he noticed she was acting strangely in the Yggdrasil's medical room.

Elly is brought to the medical room, and eventually, she wakes up with seemingly no memory of what's happened. Sigurd enters the room and says that the radar has picked up signals of a giant Gear heading straight towards them. Bart decides to assist in protecting the Thames as thanks for all their help, and Citan also decides to bring Elly along so she can prove herself trustworthy.

Chapter 33: Ramsus' Attack

Dominia tries to attack the Yggdrasil in her own Gear; however, she is swiftly defeated by the party. Suddenly, shots begin narrowly missing the Yggdrasil from underwater. The party dives into the water with their Gears and they find that the ones attacking them are Ramsus and Miang inside the Haishao. Ramsus says that he's been looking for Fei, and that Fei is his arch-rival who must be eliminated. He also asks Fei what happened to his "other Gear", to Fei's confusion. Ramsus critically injures Fei, but Elly stops Ramsus from killing him using her Gear's Aerods, a powerful ether drone attack. This attack destroys the main tank in the Haishao, forcing Ramsus and Miang to retreat.

Fei is brought to the Thames' sick bay and is placed on life support due to his immense injuries. The doctor onboard says that Fei has a chance of survival if he is brought to the infirmary at the Ethos headquarters. However, ordinary people are not allowed access unless granted special permission by a member of the Ethos. On the bright side, the doctor mentions that an Etone, a special kind of priest from the Ethos known as the atoners of sin, will be visiting the Thames. The doctor explains that the Etone is coming to perform an investigation and that Etones are the ones who cleanse the Wels, mutants also known as "Reapers" that have recently been appearing in Aquvy. Citan decides to bring Fei to the Yggdrasil, and Bart and Elly are sent out to find the Etone and ask if he will allow Fei access to the hospital.

Chapter 34: A Young Priest

Atop the Thames' deck, while searching for the Etone, Bart and Elly run into Margie, who is also searching for the Etone as she got word of the situation from Citan. She asks a man about the Etone, and he says that he saw the Etone earlier, but he has since left. Suddenly, they see two crooks attempting to kidnap a young girl, and as the party tries to intervene, a man fires a warning shot towards the crooks. The criminals recognize the man as someone named Jesiah, and they run off in fear.

Jesiah points a gun at Elly, calling her a "dog of Solaris". But Citan interrupts, recognizing Jesiah by his gun and his technique. He tells him to stop threatening Elly as she was only trying to help the girl, who is revealed to be Primera, Jesiah's daughter who suddenly went mute after a traumatic experience. Jesiah apologizes to the party and tells them to refer to him as Jessie. Citan asks about Jessie's family (admittedly in an unintentionally rude manner), and Jessie reveals that his wife died when he wasn't there, and that he is here because his son has "unsavory business" at the Thames. The man Margie talked to earlier interrupts telling them that the Etone has arrived.

They explain to the Etone why they need access to the Ethos' hospital. Jessie walks up, and the Etone is revealed to be Jessie's son, Billy. Billy is surprised to see Jessie, and he asks where he has been all this time. Billy also says that the Ethos has labeled Jessie as an "undesirable element", leading Billy to wonder what he's done. After hearing that Elly helped save Primera, Billy agrees to help the party, allowing them access to the Ethos headquarters. Billy leaves, and Jessie asks him to take Primera to the "brat house", and he agrees. Jessie leaves, and he says goodbye to Citan, whom he too calls Hyuga. Citan says that Sigurd has completed work on the Yggdrasil, allowing them to depart for the Ethos.

The party heads to the Ethos headquarters in the Yggdrasil, which has now been upgraded to the Yggdrasil II, allowing them to traverse through both sand and water. In the headquarters, they are greeted by Billy, and they leave Fei in the infirmary to be taken care of. On their way to check on Fei, they run into a fellow Etone, Verlaine, who reaffirms that Jessie is not a good man. Billy agrees, saying that he has no respect for his father. They reach Fei and it seems he might make a miraculous recovery, though more treatment is required. Elly blames herself for having sabotaged the Yggdrasil, but Citan assures her it wasn't her fault. Citan and Bart go for a walk, while Elly stays in the infirmary by Fei's side.

After some time, Fei's treatment is finished; though he will remain unconscious for the next few days. Elly wishes to thank Billy for his help, but they don't know where he is. The clergyman in the infirmary says that he went to his orphanage, as he was worried about the children there. They decide to bring Fei back to the Yggdrasil's medical bay and thank Billy at the orphanage.

Chapter 35: The Orphanage

Inside the orphanage, Elly thanks Billy for his help. Billy reveals that he opened the orphanage as he and Primera haven't had parents since he was young, so he wanted to help kids going through the same situation as them. Suddenly, Sigurd comes in and alerts the party that the Yggdrasil's radar has detected a large ship. Jessie comes in as well, recognizing Sigurd. Billy also recognizes Sigurd, calling him "Siggy", which greatly upsets Bart. Sigurd reveals that Jessie was both his and Citan's senior at Jugend and that he rented a room at Jessie's home. While Sigurd lived with Jessie, Billy grew an attachment to Sigurd. Citan, Sigurd, and Jessie go to the Yggdrasil to talk over some drinks.

Eventually, the Ethos' bishop, Stone, arrives and Billy greets him. Stone says that a transport ship belonging to the Ethos that recently went missing has finally been found, but there has been no response from the crew of the ship. Stone assumes this is due to Wels attacking it, and he asks Billy to take care of the situation. Bart wonders if it's the same ship that was detected by the Yggdrasil's radar. As thanks for helping Fei, the party decides to go with Billy and help him, despite his reluctance for help.

In the Yggdrasil's gun room, Citan, Sigurd, and Jessie are all discussing their past in Solaris; saying that Ramsus felt betrayed when Sigurd left. The rest of the party enters the room and tells Sigurd that they must depart for the Ethos transport ship. Jessie decides to leave, when suddenly, a drunken Sigurd falls over, leading them to delay their trip until tomorrow. Jessie comes back to the orphanage and tells Billy that he should stop being a priest, but Billy gets upset by this and says that he doesn't want Jessie in his life anymore. However, Jessie says that Billy just doesn't understand the truth yet, and that Billy's mother, Racquel, died in vain. This leaves Billy confused, and Jessie decides to leave.

The next morning, the party finds Billy in the Yggdrasil, and Elly asks him why he became an Etone. He proceeds to explain; When Billy was young, Jessie left the family and completely disappeared. A few years later, his mother, Racquel, was killed when Wels attacked their house. Stone proceeded to enter the home and kill the Wels, saving Billy and Primera. Unfortunately, Primera has never spoken since this incident. Stone's act of heroism inspired Billy to help people in need too, so he left Primera in the Ethos' care, and proceeded to train to become an Etone at the monastery. After he finished his training, Billy returned and opened the orphanage. Unexpectedly, Jessie returned too, though he appeared and acted much differently. Due to this, Billy is unable of viewing him as a father, though Primera still has affection for him. They proceed to depart for the transport ship.

Chapter 36: Reaper's Ship

They enter the transport ship, which is in very poor condition following the attack. As they venture deeper, they are attacked by a large Wels. They swiftly defeat it, however it calls for its "buddy" to come over. Preparing in case of another large Wels attack, Billy signals the kids back at the orphanage, and all of the kids at the orphanage gather together. Using a very unconventional method, they manage to raise Billy's Gear, Renmazuo, out of a storage hatch in the ground, and launch it to the transport ship. Billy's Gear arrives at the transport ship and picks up the party just as the giant Wels begins to attack them. Billy lands his Gear on top of the Yggdrasil and the party battles against the Wels.

After defeating the Wels, Billy thanks everyone, and he says that he must return to the Ethos headquarters to report the job results.

Chapter 37: Burning Souls

Upon entering the Ethos headquarters, the party sees multiple corpses scattered across the ground. On the ground, Billy finds shell casings belonging to Jessie's gun, leading him to believe that Jessie is responsible for the attack. As the party continues ahead, they encounter the Ethos' Pontiff being cornered by assassins. The assassins reveal that the Ethos rebelled against them, which sparked the motive for the massacre. Shortly after, the Pontiff is killed, and the party kills the assassins.

Eventually, the party finds themselves inside the Ethos' data bank; a room only high-ranking officials are allowed access to. Elly recognizes that the room is full of high-tech equipment from Solaris, which comes as a surprise to everyone, including Billy. Citan and Elly begin looking at the information stored in the database, and they discover that the Ethos is a subsidiary organization of Solaris. They also discover that 500 years ago, during the aftermath of a war between Solaris and the land-dwellers, Solaris founded the Ethos to control and supervise humans on the surface as a means to prevent them from revolting against Solaris again. The Ethos has been sending supplies to Solaris, and they've even sent land-dwellers to Solaris for manual labor and testing. Lastly, Citan discovers a plan initiated by the Ethos without Solaris' knowledge; In an attempt to become independent from Solaris and pursue world domination, the Ethos has been excavating resources and weapons from the ruins of Zeboim, a 4,000-year-old technologically advanced civilization that has sunk to the bottom of the sea.

Outside the data bank, Billy finds himself questioning his faith, and the party is approached by Verlaine, who threatens to kill Billy as a means of "cleansing" him. Before he can do anything, Jessie arrives and shoots Verlaine's assistant with a stun bullet, and he reveals that Verlaine is part of a Solaris assassination unit working under Stone. Verlaine affirms this is true and says that the Ethos doctrine was created to deceive the masses. He also says that the Ethos have been perpetuating meaningless wars that send battle data to Solaris and keep land-dwellers distracted from them.

As Verlaine begins to reveal too much critical information, he is killed by Stone and his assassins. Jessie says that Stone hasn't changed, and refers to him as "Stein". Stone threatens to kill Jessie, but he decides to leave and have his assassins attack the party. After defeating the assassins, the party decides to chase after Stone. They follow him into a hangar, where they see him escaping in Alkanshel, a giant white Gear. They decide to pursue him, as they fear the Thames might get attacked as part of Stone's goal to destroy the Ethos and its affiliates.

Back onboard the Yggdrasil, the radar detects a large ship above the Thames. Above the Thames' fleet, a fishbowl-shaped ship shoots multiple beams, destroying the fleet. The Gazel Ministry discusses the Ethos, calling them an expendable group, as they have already fulfilled their purpose for Solaris. They also discuss Krelian's goal to obtain a "molecular machine". However, they don't understand why Krelian places importance on it, as they believe that humans and machines are the same.

Krelian decides to drop Wels on the Thames, and he also receives word that troops are entering Zeboim; which greatly pleases him. On the Thames, the captain questions why the Ethos would attack them, and begins preparations to fight against the Wels and assist the survivors from the destroyed ships in the fleet. The party goes to the Thames to help.

Chapter 38: Ocean Floor

Citan greets the Thames captain, and despite their incredible powers as men of the sea, the Thames' crew suffered multiple causalities and injuries from the attack. The captain says the fishbowl-shaped ship is heading to a remote excavation site, which he finds odd, as the site supposedly contains nothing of value. Some Thames crew members reported seeing Stone's Gear leading the fishbowl-shaped ship to the excavation site. The captain says the Thames will help the party in any way they can, and the party decides to follow in pursuit of Stone and the fishbowl-shaped ship.

Chapter 39: Deep Sea Girl

The party arrives at the Ethos Dig Site and goes deep underground in an elevator. Meanwhile, Grahf sits underwater in his Gear. He remotely speaks with Miang, who tells him that Fei's friends are heading to Zeboim. She also says that "his Gear is reawakening", and that "he himself will awaken also". After hearing this, Grahf takes off in his Gear.

Deeper inside the dig site, the party finds themselves in a giant city underground. Eventually, they find a laboratory, and they discover a test tube with a girl inside it. Citan realizes the girl is an artificial lifeform, but he is interrupted by Stone and his assassins entering the room. Stone says she is comprised of a nanomachine colony, and that the girl will lead to humanity's salvation. He awakens her from the reactor, attempting to take her. He reveals his intentions to bring the girl to Krelian and quickly leaves with the girl.

As he's leaving, Stone brings in two of the Elements to prevent the party from chasing after him; Tolone and Seraphita. After battling against the party for a while, Tolone and Seraphita withdraw from the fight, as they have already created a big enough distraction. The party decides to pursue Stone. Meanwhile, Fei is lying in the Yggdrasil's medical bay, and he has a vision of a man who looks like himself locked in the room with the nanomachine-comprised girl. He sees the lab being raided by soldiers, and also sees a woman who looks like Elly being pinned down by the soldiers as she begs them not to take "their child". After this dream, the Yggdrasil's doctor notices Fei is missing from his bed and wonders where he went.

The party catches up with Stone, but they mysteriously hear a voice telling Stone to give the girl back. Suddenly, a strange-looking man piloting the same red Gear the party saw at the Aveh-Kislev border intervenes. The man asks for the girl back, saying that it belongs to him. After asking for his name, the man refers to himself as Id, and he proceeds to battle the party. Wiseman abruptly appears in his Gear and he holds back Id, allowing the party to quickly escape. Stone also takes this opportunity to escape, and Wiseman encourages the party to chase after him. As they go on ahead, Wiseman and Id proceed to battle.

Outside the dig site, the party realizes they were too late, as they see the fishbowl-shaped airship leaving. Citan fears that Solaris intends to research the girl and use her to further their nanomachine technology. Back at the Yggdrasil, the party finds Fei awake standing in front of his Gear. Suddenly, Stone's Gear is spotted directly ahead watching over them. Citan brings Fei back to the infirmary to rest, and the party goes to confront Stone.

Grahf appears in his Gear and powers up Stone, whose appearance has drastically changed to a monstrous form due to his body having been altered by Krelian. The party fights the powered-up Stone, but they struggle to defeat him due to him being surrounded by an ether barrier. Stone reveals the truth to Billy; Stone is jealous of Jessie, as he had gotten into a relationship with Racquel, Stone's love interest. Jessie and Stone also competed for command of Gebler, only for Jessie to take command and leave Solaris shortly after. After this, Stone went to the surface and arranged for Wels to kill Racquel, as she reminded him of Jessie. He also reveals to Billy that the Wels he's been purging are actually humans mutated by Solaris.

Jessie shows up in his Gear, the Buntline; a Gear designed by Citan with the ability to transform into a cannon that another Gear can use to launch the Buntline's pilot as a bullet. Using this ability would destroy the ether barrier around Stone, but it would likely result in Jessie's death. However, Billy decides to go through with the plan, as he is unaware of the risks. Using the Buntline as a cannon, Billy launches Jessie at Stone, destroying the barrier. Citan tells Billy about the Buntline's functionality, leading him to realize that Jessie died. With the barrier dispelled, the party finishes off the Alkanshel, killing Stone.

Shortly after, the party mourns the loss of Jessie, but Billy decides this was a good way for him to go out. However, Jessie walks up behind them, revealing that he's still alive since he modified the Buntline to prevent its pilot's death. After everything, Primera says her first words since Racquel's death; "Papa".