In the beginning, Deus was created. This has made a lot of people very angry and has been widely regarded as a bad move.
The creation of an unknown spacefaring civilization, Deus was originally intended to serve as a biological weapon. To power Deus, an entity known as the Wave Existance is summoned from another dimension and trapped inside Deus's engine, Zohar. However, its creators deem Deus too powerful to use, and they attempt to dispose of it by shipping it away on a spaceship called the Eldridge.
Deus, being a sentient organism, discovers the plan to eliminate it and attacks the Eldridge in transit. After much gratuitous usage of the word "evacuate", the Eldrige crashes on a nearby planet. The sole survivor of the crash is a young boy -- the first incarnation of Fei -- who was left crying for his mother.
Although its physical form was trapped inside Zohar, the Wave Existance is able to instill its power in the boy, who had looked upon it during the attack, in an effort to destroy Deus and free itself. The Wave Existance than creates a woman -- Elly -- in the image of Fei's mother and gave her its will.
In order to defend itself, Deus used part of itself to create the first humans -- Cain, the Gazel, and Miang. Miang possesses the Ouroborous (or Urobulos according to Professor Daravon ^_^) Gene, which is passed on to all the women in the world, as they were all descended from her. This gene allowed any woman to become Miang, thus guaranteeing her immortatilty.
The next time we see Fei and Elly, they are in their second incarnation (the Wave Existance keeps reincarnated them); Fei is called Abel, and Elly is Elly as always. They are running from Cain, who kills Elly.
Fei and Elly's third incarnation occurs in the Zeboim civilization (which I think is supposed to be present-day Earth). Here, people live in flying cities above the ground and fight with giant robots called Gears, which use the energy emitted from Zohar to function. However, genetic flaws have rendered many people, including Elly, unable to have children. Kim (Fei), who seems to be a scientist, creates an articial human with self-healing nanomachines, whom he names Emeralda. Just then, guards burst in and kill Elly, and presumably Kim as well.
When the fourth incarnation rolls around, only one flying city remains from the collapsed Zeboim civilization: Solaris, ruled by Emperor Cain and the Gazel Ministry. Solaris rules the world below, but a band of rebels, including Lacan (Fei's fourth incarnation), Sophia/Elly (her real name seems to be Elly, but she is known as Sophia in Nisan), Krelian, and Roni and Rene Fatima are fighting against them.
The land-dwellers are aided by Shevat, a new flying city being constructed atop the Tower of Babel (which is also part of the Ft. Jasper weapons system) under the supervision of Queen Zephyr. Shevat is also home to three Gurus -- Gaspar, Taura Melchior, and Balthasar. Taura teaches Krelian about nanotechnology.
Shevat, however, decides to reveal the position of the rebels to Solaris in exchange for their own safety. Solaris promptly attacks the rebel camp in Nisan, catching the troops off guard. To defend her people, Sophia/Elly sends her ship on a suicide run at the Gebler forces. Her comrades escape, but Krelian goes postal and runs off saying that if there must be no god and he will create god himself. Lacan also goes berserk, and is transformed by the Wave Existance into two parts -- his body becomes Grahf, while his soul is passed on to the next incarnation.
Soon thereafter, a bunch of mysterious monsters called the Diabolos appear and attack the world. Solaris and the land-dwellers call a temporary truce to their fighting to fight the Diabolos. With the power of the Omnigears, such as Roni's Andvari, the humans win. During the conflict, however, the Gazel are killed, and their personalities are stored in the data banks of Solaris's SOL-9000 computer.
In the aftermath of the war, Solaris sets up the -Ethos-, a faux religion with which they control the earth-dwellers, and begins using its Soylent System to turn the test subjects of its genetic experiments into food products or Wels. A special drug, the Limiter, is placed in the food, which renders those who consume it -- all the land-dwellers -- unable to resist Solaris.
As the loser of the war, Shevat goes into hiding by concealing itself behind its Gate. Roni and Rene found Aveh, and Kiselv is also founded by some other guy (we don't know who). Meanwhile, Krelian has joined Solaris to pursue his mission of resurrecting Deus.
Several hundred years later, things have changed little. Solaris has been manipulating a war between Aveh and Kislev on the surface to prevent the earth-dwellers from gaining in power. Krelian, who is pulling all the strings in Solaris, attempts to create a Contact for the Wave Existance. He genetically engineers a clone of Cain that features all the best traits of humanity -- Ramsus -- in hopes that he will be able to contact the Wave Existance. He soon discovers that Ramsus is not needed, as the real Contact has been born to Wong Khan and Karen, agents of Shevat.
Miang takes over the body of Wong Karen and begins subjecting Fei to psychological tests to determine if he is really the Contact. Time again and time again Fei destroys the Solaris researchers who try to probe his mind.
Grahf, who has gone through several bodies in his quest for destruction, hears of Fei's birth and journeys to the Wongs' home in Lahan in order to claim the body of the new incarnation of Lacan. He uses his powers to draw out Fei's inner power, and he (Fei) unleashes a blast of energy that kills Karen. Grahf then spirits the 'awakened' Fei away and makes him his right-hand man.
Meanwhile, in Aveh, the Fatima Dynasty is overthrown by Shakhan, an Ethos bishop who has the backing of Solaris behind him. King Edbart is killed, but his sons Bart and Sigurd, and retainer Maison, escape in the Yggdrasil, the Aveh flagship, and go to live in Nisan. Solaris sends General Vanderkaum to control the Gebler forces.
Sigurd, however, is abducted by Solaris and forced to join Jugend, their military academy. He eventually joins the Elements force, along with Hyuga Ricdeau (Citan), Miang (in yet another new body), and Jessiah Black. Hyuga/Citan and Sigurd are both supporters of Ramsus's rebellion against the Solaris class system.
Ramsus is called into action when Grahf and Id attack Elru on the surface. Id single-handedly trashes Ramsus's Gear battalion, and the entire country is destroyed. The only survivor is Dominia, who joins with Solaris and later becomes part of the Elements after Jessiah quits to live on the surface with his wife Racquel.
Wong Khan catches up with Id and Grahf and somehow seals the Id part of Fei's personality inside and constructs a new persona over it. This persona, the Coward, refuses to acknowledge what he has done, however, and creates a third persona -- the "normal" Fei -- to deal with his problems while the Coward relives the memories of his childhood. Meanwhile, Grahf takes over Khan's body, but his control is incomplete -- during lapses of Grahf's control, Khan returns to his normal self, and, during one of these periods, he brings Fei to Lahan Village and leaves him there in the care of Chief Lee.
Sigurd regains his memories of his life on the surface and escapes Solaris to return to aid Bart. He, Maison, and Hans the penguin use the Yggdrasil to prey on Aveh and Kislev troops, thereby keeping either side from becoming too strong and keeping the balance of power.
Also defecting from Solaris is Nikolai Balthasar, son of Shevat's Balthazar. He attempts to flee to Shevat after finding out what Krelian had planned for his Gear research (Deus's revival), but is killed in the attempt and has his mind implanted into the Achtzehn Gear. His daughter Maria manages to escape in the Achtzehn's sister Gear, Siebzehn.
Citan remains behind in Solaris, but is later send to the surface by Cain on a mission to spy on Fei and determine whether he poses a danger.
While not in Khan mode, Grahf is scheming to get Fei back under his control. He has the Kaiser of Kislev manufacture a Gear to his specifications, then arranges for a Gebler force from Aveh to steal it and land in Lahan. A battle ensues, during which Fei hops on board the Weltall, as planned, and uses Id's power to destroy Lahan.
Forced out of the village by the survivors, Fei journeys south through the Blackmoon Forest, where he meets the fifth incarnation of Elly, a Gebler officer and the leader of the group that attacked Lahan. After Fei "saves" her from some really wimpy monsters that she could have beaten on her own, she travels with Fei for a short while. That evening, Citan shows up and recommends that Elly leave and return to her family in Solaris. She reluctantly agree.
Citan and Fei are hunting for parts for the damaged Weltall when they are captured by an Aveh transport that was seeking the Weltall. The transport is in turn attacked by the Yggdrasil, and Fei and Citan are brought aboard. They agree to help Bart in his mission to rescue Margie, who has been captured by Shakhan.
The trio frees Margie (and Chu-Chu ^_^) from Fatima Castle and escapes back to Nisan to plan their next move. Meanwhile, Ramsus is appointed head of the Gebler forces, and Vanderkaum is demoted to border patrol.
To overthrow Shakhan, Bart and Citan sneak into the castle, while Fei causes a distraction at the Kislev border. Shakhan sees through their plan and surrounds Bart's team, and they are saved only when Maison rescues them in Citan's Land Crab. Fei meets with more success, as he destroys the Gebler flagship Kefeinzel and Vanderkaum's Gear, the Dora. Grahf then shows up and gives Vanderkaum "the power", forcing Fei to transform into Id. Id then annihilates Vanderkaum, Bart's troops, and the Yggdrasil, and severely damages Ramsus's Gear. Citan evacuates the Yggdrasil as it goes down and heads to Nortune to find Fei.
Fei is picked up by some Kislev soldiers and, at Miang's request, is transferred to the prison block of Nortune, the capital of Kislev. Grahf also has the Battling committee actively recruit Fei, and then arranges for the Weltall to be given to him when he enters. Little does Fei know that the Weltall has been rigged to overheat during the match, thus putting Fei out of comission. While unconscious, he changes into Id and kills Rico's men, believing them to be responsible.
After Fei wakes up, he is confronted by Rico, who informs that he is being held responsible for the death of the sewer guards. Rico, Fei, and Citan go to the sewers to investigate and fight and kill a monster called Redrum (actually one of the Wels), thus "solving" the mystery. Rico's arm is wounded during the battle with Redrum, however, thus allowing Fei to defeat him in the Battling tournament and become the new Battling champion.
Meanwhile, the Ethos is plotting to eliminate Kaiser Sigmund, as he has been acting too independtly from Solaris. They rig Rico's Gear to go berserk and attack the Kaiser's box, but the Kaiser narrowly escapes death. For this incident, Rico is sentenced to be executed, but he ends up being rescued by Fei, Citan, and Hammer.
Growing desperate, the Gazel order the entire city bombed into oblivion. The Elements and Elly's Gebler squadron are assigned to carry out the mission, but Elly defects to Fei's side and aids him and Rico in directing the Hecht off course. Grahf shows up at the last minute to save Elly.
Back in Aveh, Bart and co. miraculously survive the sinking of the Yggdrasil when they end up in an underground cave containing another Yggdrasil, dating back to Roni's era. This one is designed for sea travel, so Bart's band hits the seas and shoots down Kislev's new Goliath airship on its way to Aveh... only to discover that it was actually Fei and his friends, trying to escape from Kislev in the stolen plane.
Fei and Elly are rescued by the Thames, a floating town commanded by the "Man of the Sea". The Thames is currently working for the -Ethos-, which is trying to excavate some Zeboim ruins in order to acquire technology that would allow them to break away from Solaris.
Bart shows up in the Yggdrasil and apologizes for shooting down the Goliath. After a number of failed attacks by Solaris, Ramsus eventually manages to succeed in injuring Fei in combat. Seeing that Fei's wounds require medical attention, the party seeks the help of the healers at the Ethos. While still on the Thames, they meet Billy Lee Black, a priest/exorcist from the -Ethos-, when they save his sister Primera. Billy agrees to help Fei, so they take him to the -Ethos- Headquarters, elsewhere in Aquvy, and have him treated by the doctors there. He is promptly released and taken back to the Yggdrasil sick bay.
In gratitude for Billy's help, the party agrees to accompany him on a mission to destroy a Solaris ship infested with Wels mutants. The mission is a success, but when Billy returns to the Ethos HQ, he finds everyone dead. The attack is the work of his mentor Bishop Stone, who killed all those who were attempting to break away from Solaris. Stone escapes in his Alkanshel (I think that's supposed to be "Archangel") Gear to attack the Thames.
During the battle, the Alkanshel is joined by a black "fishbowl" device (I believe it's the Soylent System) that drops out Wels. The Thames manages to fend off the attack, but not without being damaged. Citan and the gang follow the "fishbowl" to a supposedly-abandoned Solaris dig site, where they discover Emeralda, still left in the tube that she had been created in 4000 years ago. But before they can free her, Stone arrives and captures her, so that Krelian can use her in his nanotechnology experiments. While the party is pursuing Stone out of the dig site, Fei suddenly shows up in Id form and demands that Stone release his daughter. Stone escapes, and suddenly Khan/Wiseman shows up to hold off Id while the party escapes.
Back on the Yggdrasil, Fei turns up at the Gear Dock at loss as to what happened to him. Then Stone, now merged with his Gear, attacks, but Billy and Jessie team up to put him out of commission. The party then goes to Shevat to ally with Solaris's rival. There they meet Maria and Queen Zephyr. Meanwhile, Dominia sneaks into the city and shuts off the shield generators, allowing Solaris to attack.
Fei and friends fend off the initial assault, but then the Achtzehn arrives and uses its Psycho Jammer to freeze the Gears. Enter Chu-Chu, who uses her "Churansformation" to assume the size of a Gear and fend off the Achtzehn. Nikolai then transfers his consciousness from Achtzehn to Siebzehn, and has Maria destroy Achtzehn.
Back on the surface, Shakhan's forces invade Nisan. Bart rushes to Nisan and enters the underground Ft. Jasper, where he discovers Roni's Andvari Omnigear. As Ft. Jasper is raised from the ground, Shakhan attacks it, but is forced to retreat. Bart chases Shakhan to a cave and finishes him off, also destroying one of Solaris's Gate generators in the process. Meanwhile, Bart's soldiers retake the capital, and Bart assumes the throne.
To destroy the second Gate, Billy fires a beam from the recently-excavated Ft. Jasper. It bounces off the lens on Babel Tower, designed for just that purpose, and demolishes the Gate under the -Ethos- HQ. The last Gate lies underwater at Sargasso Point, so Fei and co. dive down to destroy it. Along the way, they encounter Emeralda, who is under Krelian's control. After destroying the Gate, they convince Emeralda to come back with them to the Yggdrasil.
With all three Gates destroyed, Solaris appears in the sky. Fei and Elly sneak into the capital district, and after being chased by some Security Cubes, make their way to Elly's house. They attempt to use Elly's father's computer, but are caught by Erich. To Fei's surprise, Erich lets him go and tells him to follow his own path.
Elly stays behind at her house, but soon some Solaris soldiers arrive and demand that her parents turn over Elly for her traitorous acts. Erich stalls the soldiers while Elly escapes. She catches Fei and Citan on their way into the palace via a dust chute.
In the palace, Elly confronts Citan with the accumulated evidence that he is working for Solaris. Before Citan can reply, the lights go out. In the dark, Fei stumbles into the SOL-9000, and is captured. Meanwhile, Citan frees Elly and the rest of the party, who was captured earlier, and removes their Limiters. Hammer is confronted by Krelian, who threatens to mutate him unless he carries out his orders: To capture Elly, whom Krelian needs to resurrect Deus.
Hammer is forced to comply, and while the party is making their escape with Elly's parents, he suddenly points a gun at Elly. Medena forces her way into the path of the gun and advances on Hammer. Hammer panics, shoots her, and runs off. Just then, Grahf and Miang show up and kill Erich in an effort to 'awaken' Elly. They meet with no success, but Fei is 'awakened' and turns into Id. He then destroys Solaris completely, though all of the major villains escape.
Shevat insists on carbon-freezing Fei to prevent him from using his Id power again, but Elly frees him. They fly away in Weltall, but Ramsus arrives. Since he last fought Fei, Ramsus has learned that he was an artificial Contact created and was "discarded" once Fei was discovered, and now is obsessed killing him. Using his new Omnigear, he shoots down Weltall.
After their crash landing, Fei and Elly are nursed back to health by Taura Melchior, who lives in seclusion on the surface. Elly, Citan, and Emeralda fire the Limiter cure out of a cannon to spread it across the world, while Fei hurries off to Kislev to stop a last-ditch attack by Solaris. He and Bart combine the Imperial District with the Yggdrasil to form a Gear and destroy Solaris's Fort Hurricane.
Krelian activates the Soylent System and starts mutating people into forms in which they will be able to be assimilated by Deus. While the sisters of Nisan try to cure the mutated people, Fei and company destroy the Soylent System and the Sufal Mass, a huge creature formed of amalgamated mutants.
While Fei and co. search for the remaining Anima Relics that they can use to enhance their Gears, Krelian convinces Ramsus to kill Cain -- as a clone of Cain, Ramsus is the only one who can kill him. Krelian also melds Hammer with a Gear and sends him after Fei, but Hammer is killed.
With Cain out of the way, the Gazel are able to use the Gaetia Key to raise the Eldridge from the sea -- and, in turn, Krelian summarily erases them from the data banks, leaving him in command. Fei shows up in the Eldridge to prevent Krelian from locating Deus's shell, but Grahf takes him captive and tries to crucify him. Elly comes to the rescue in her Omnigear and succeeds in rescuing Fei, but then she is captured by Krelian and Grahf.
Krelian begins construction of Merkava, the "ark of god", which he will use to return to the dimension the Wave Existance is from. Fei and Ramsus attempt to stop him; Ramsus kills both Krelian and Miang, but Krelian has already merged with Deus, and Miang merely assumes the body of Elly. Enraged, Fei turns into Id again and is once again carbon-frozen.
While Deus starts assimilating the people of the planet, Id breaks out of his prison and destroys Shevat. Citan and the other characters catch up with him on his way to Contact the Wave Existance. With the aid of Khan, Fei eventually resolves all his multiple personalities, then the Wave Existance appears and changes the Weltall into the Xenogears.
Grahf takes over Khan's body again and tries to kill Fei. Then Deus strikes, however, attempting to destroy Fei before Fei does the same to Deus. Grahf/Lacan/Khan sacrifices himself as a decoy Fei, while Fei and his friends return to Merkava to destroy Deus. They succeed in destroying Zohar, the core, thus freeing the Wave Existance. The energy emitted by the Wave Existance threatens to destroy the world, so Elly (now part of Deus) uses her powers to move Deus out into space.
With the destruction of Zohar, all the Gears have stopped working, except Fei's (which has evolved due to his Contact). Fei blasts out into space after Deus and ends up being sucked into some super-duper dimension, where he must battle the Ouroborous gene itself to return Elly to normal. He succeeds in rescuing Elly, and he and Elly return to the planet as Krelian dies. The end.