"Gilgamesh and Balarant. For one hundred years now, these two star systems have been locked in a war whose cause was long ago forgotten. At first they managed to contain the hostilities. But by the time I joined up, the front had enlarged...and 200 worlds belonging to them had been caught in the flames of war.

I fought. At first I fought sincerely, to defend my home world of Melkia. But the war just dragged on and on, with no end in sight. I'm so tired now. Everyone is so tired."

On the edge of the Astragius Galaxy, the decommissioned Gilgamesh battleship Teltain approaches asteroid Lido. It deploys a platoon of Scopedogs, which attack and infiltrate the base. Chirico Cuvie, an AT pilot newly-transferred to the Teltain, protests that they are attacking one of their own bases, but his platoon leader orders him to be silent while they begin looking for their objectives. Left on his own, Chirico discovers one of the objectives himself - the body of a woman, lying suspended in a tube of swirling energy. She wakes and sees him. Shocked and bewildered, he closes the tube. His mind racing with questions, he is nevertheless ordered outside - and barely escapes an explosion meant to end his life.

Lost and adrift in his damaged Scopedog, Chirico is picked up by the Melkian battleship Bauntaunt and questioned about his involvement in the Lido raid. the intelligence officer who question him, Captain Jean-Paul Rochina, is convinced that Chirico knows what happened to "the Prototype," and takes him back to Melkia for further questioning. There, Chirico escapes and flees into the vast outback. Unaware that Rochina's commanding officer, Battentain, has ordered a homing beacon planted in his body, Chirico is determined to find out what sort of mess he's been caught up in - and who exactly that woman on Lido was.

"That day, the accursed war which had so disrupted my destiny ended. But its end was ultimately meaningless for me. The moment I saw her, my own private war has begun...a war for which there would be no end."

"Chirico! Chirico Cuvie! Answer me! From where dost thou come? Who ordered you to come to Uoodo? Why are you in this city?"

Chirico thinks he hears the voice of God, but it is instead Serge Borough, who is working with Iskui for the Secret Society. Chirico is now their captive in the impregnable police tower. Outside, Vanilla plans to bust Chirico out.

Later, Vanilla bribes a cop for the blueprints to the tower, and Coconna brings Gotho to meet with him. Together, the three pool their resources and tunnel through the city's sewer system using an industrial laser from Gotho's arsenal. Just as Chirico is taken from his cell for another round of interrogation, his rescuers arrive and whisk him to safety.

They recover at Gotho's scrap yard, and a call comes in - for Chirico. He is offered another chance to fight a Battling match, this time against an unknown opponent for big money. Chirico accepts, and the opponent turns out to be Captain Oriya, another commander from Lido. Borough and Iskui watch from the shadows, determined to see Chirico die. Chrico wins again, but just as Oriya agrees to reveal the secrets of the mission, Iskui orders his troops to open fire. Chrico barely escapes, and spots a limousine driving away, carrying The Phantom Lady in its back seat. Her presence here cannot be a coincidence.

"As I saw the limousine speed away through the flames, I couldn't help thinking how incongruous it looked amidst the battle..."

During the battle, Gotho managed to make off with the payment Iskui originally promised him, but he didn't hang around to see if Chirico made it out. Having rejoined Vanilla and Coconna, he gleefully counts his money. But they all grow uneasy as more time passes without Chirico returning. Later, they learn that he won't be coming back; he is now a police prisoner. Coconna is adamant that they have to go to Chirico's rescue.

They make an attempt to disrupt the police caravan that is taking Chirico to headquarters, but their first flyover in the stolen helicopter is unsuccessful. Gotho and Vanilla are ready to take their money and run - and Coconna realizes the money is what will give them the means to help Chrico after all.

Sometime later, they fly over the caravan again...but this time instead of attacking, they dump their money out the window. Predictably, the Uoodo streets fill with people, stopping the caravan dead in its tracks. This time it works - Chirico breaks free and escapes back to Vanilla's home with the others. Acknowledging their sacrifice, he finally begins to feel trust and friendship.

"Friends. I was almost embarrassed to feel it. But a long dead warmth had begun to rekindle somewhere in my heart."

"Oppressive heart and dampness. Jungle disease and deadly insects. It may have been painted in tones of green, but this was definitely another province of hell. But to me, after dodging death and my pursuers for the three months since I left Uoodo, the war-torn Kingdom of Kummen seemed like heaven."

Rochina and Battentain continue to monitor Chirico via the homing beacon implanted in him. They watch with interest as he enters Kummen and the civil war that is raging between the mercenary forces and the Holy Kingdom. Chirico signs on at the mercenary base Assemble EX-10, and is reunited with Gotho, who has been waiting for him since the fall of Uoodo. Chirico is then approached by Kan Yu, and interrogated about the beacon they have discovered in his x-rays.

Queestioned by Gon Nu about his purpose here, Chirico answers that he has seen the Perfect Soldier, and is searching for it in Kummen. Gon Nu knows of the PS and lets Chirico off the hook, but Kan Yu remains suspicious of his motives. That night, Gotho drives Chirico into Niitan, a nearby town, where he has bought a nightclub called "The Fantom Club." Vanilla and Coconna are overjoyed to see Chirico again. Kan Yu enters the club and begins to taunt Chirico, but they are interrupted by explosions outside - the last artillery attack by the fearsome Veela Guerrillas!

Chirico joins other mercenaries as they scramble for their ATs and pluge into the jungle. The Guerrillas have deployed Turtle-series ATs against the mercenaries, and the two forces seen evenly matched except for one wild card: a deadly blue Turtle nicknamed the "Blue AT." Chirico faces off against it in his Marshydog, and is positive he knows who the enemy pilot is.

"In that instant, I knew for certain. Its reaction time was too fast to be a normal human. The one I was fighting had to be her. The woman I'd lost at Uoodo. My Fyana."

An air patrol from EX-10 locates Chirico and brings him in to the EX-10 hospital. Gotho, Vanilla, and Coconna stand vigil over Chirico as a doctor explains to Gon Nu and Kan Yu that Chirico suffers from exhaustion and cannot answer their questions. It is actually a ruse, and the doctor is bribed to maintain it. Chirico tells the others that he has located Fyana, and Coconna fumes with jealousy.

At the Holy Palace, Kanjelman fights Ypsilon in a Balancing match. This time, Ypsilon is beaten, and Kanjelman cautions him against excess pride. Ypsilon confronts Fyana about her treachery in allowing Chirico to escape, and Kanjelman conducts a meeting with his advisors to plan a new assault on EX-10.

At the base, Gon Nu takes a leave of absence, and Kan Yu is left in charge. Observing this, Gotho promises to dig up more information and contact Chirico later. That night, Chirico sneakes out of the hospital to Gotho's house and receives a phone call. Gotho tells him that Gon Nu has gone to set up an alliance with the Melkian army, which can only escalate the civil war. As Chirico hangs up the phone, Kan Yu and his troops barge in to take him captive.

Learning of this, Kiderra and Potaria force their way into Kan Yu's office, where he is attempting to interrogate Chirico. No sooner have they freed him when an alert sounds; Veela Guerrillas are launching an attack! In the Fantom Club, Vanilla and Coconna also take notice of the attack - missiles are streaking right into Niitan!

Kan Yu scrambles his AT platoons to the base perimeter, but no enemy is in sight. Chirico realizes the truth of what is happening; the guerrillas are concentrating their attack on Niitan instead of the base. Defying Kan Yu's orders, he and his companions race to the aid of the town, hoping it isn't already too late.

"With a roar, everything began to move. I couldn't see what was ahead, but everything right now was connected into one thing. And then I knew this was all just a prelude to an approaching hell."

Lost and exhausted, Kan Yu stumbles through the Kummen jungle from one pitfall to another. He runs right into a Veela platoon and very nearly loses his life...until Shako appears out of nowhere and saves him. Later, he wakes up in the EX-10 hospital to seek Gon Nu standing over him. He will soon be back in action; the Melkian army is nearly ready to launch their attack on the prince's palace.

With Potaria's knowledge of the area, Chirico's group hijacks a Veela AT truck bound for the palace and takes it over, sacrificing Kiderra's and Potaria's mercenary ATs in favor of Veela Turtles. On the Palace ground, Monica wanders aimlessly, confused by Kanjelman's orders to abandon guerrilla warfare. Others speculate that he is giving up the fight, so she decides to find out for himself. She arrives just in time to overhear a conversation between Boorough and the prince, who states his belief that his kingdom is doomed, and that he has called all the guerrillas back to die with him. Shocked, Monica can only run.

Chirico's group smashes their way into the place grounds. Potaria leaps out of his AT and dashes into the palace on a mission of his own. Ypsilon is anxious to go and fight Chirico, but Borough orders him to wait until his new AT arrives. Tearing through palace corridors in search of Kanjelman, Potaria runs into Monica, who gets caught in a crossfire. Potaria drags her to safety, and she tells him of the prince's treachery...just before she dies in his arms.

In the skies above the palace, countless enemies appear; the entire fleet of mercenary ATs from EX-10 is preparing to attack. The battle begins in earnest, and Chirico looks up to see yet another object approaching from on high.

"There was no way of my knowing at the time...that the light I saw was a new custom AT made for Ypsilon..."

Chirico recovers after all and join Fyana in another attempt to hold off the enemy. The battle is fierce, but this time Chirico is not up to it. He is hit again, and Fyana pulls him inside as the Balarant Fatties swarm the ship. Their disappearance is reported to the Balarant patrol fleet captain, who orders his men inside to capture their mysterious opponents.

Fyana evades the Fatties as they comb the inside of the ship for her and Chirico. She finds her way to the infirmary for medication, and Battleship X makes a move of its own, firing its engines and moving off in a new direction. While some of the invading Balarant ATs attempt to disable the engines, Fyana returns to Chirico and revives him with the medicine she obtained. He laments his own helplessness, saying that Ypsilon would never fail her...and he slips back into unconsciousness as she prepares to face the approaching enemy. Fyana now fights alone, both on foot and in a Scopedog, pausing only to wonder again who placed her in this situation.

Not far away, the Secret Society follows the battle in their own ship, the Teltain. Captain Futtor keeps watch as Arron and Gurran put Ypsilon through a battery of emotional tests and discuss the prospect of a rematch between him and Chirico. Far ahead, a planet looms in the distance, and Fyana cares for a sleeping Chirico. They have faced much already, but the worst is yet to come.

"I've wandered the depths of hell. Its hot, suffocating depths. And in the distance, a light. Our ship, as though following a beckoning beacon in the night, drew us ever closer to the planet that lay before us."

Chirico and Ypsilon unleash heavy fire, with Ypsilon pausing only to eliminate anyone who threatens to interfere in their battle. Suddenly the entire room starts to shake, and the floor drops out from under their ATs - their battle has ignited the ammo dump! Plummeting helplessly, they disappear into a deep shaft, and Rochina managed to escape with Fyana as the entire building crumbles.

Landing relatively intact, Chirico gets the upper hand against Ypsilon, but does not choose to kill his foe. Instead, he begins to dig himself out and suggests they work together to survive.

On the surface, Rochina orders his men to begin an excavation and recover Chirico. He discusses the situation with Fyana, who suspects that he is hiding the answer to a key question: how has Chirico, an ordinary human, lasted so long against Ypsilon, a Perfect Soldier?

Similar questions burn through Ypsilon's mind as he and Chirico make their way toward the surface. The PS angrily declares himself a superior being, and that he belongs with Proto-One. Chirico corrects him on the name, and Ypsilon demands to know why he calls her Fyana - a question Chirico is unable to answer. Finally, when they reach the upper limits of the shaft, Ypsilon admits that they are alike in one respect; Chirico can fight as well as he can...but Ypsilon will eventually kill him.

On that note, the Balarant excavation team finally breaks through from above and rescues Chirico. Ypsilon slips away just in time to join up with a rescue team from the Teltain, and they fight their way free. Chirico is taken to Rochina, who demands that he be ready to fight Ypsilon again. In return, Rochina orders Gotho, Vanilla, and Coconna flown out of danger.

"It seemed Rochina had kept his promise. My final battle with Ypsilon. The time was fast approaching. Will I survive it, or will he? And if I do survive, what then?"

Chirico is left alive with Shako in the tunnels, but Arron and Gurran inexplicably re-materialize 800 km away in the streets of Gomor. They report this to Killy, who is amazed to finally learn one of the secrets of ancients Quent: teleportation.

Chirico and Shako return to Meji for an explanation of what happened, but he cannot answer. Chirico asks where a power generator might be found, and Meji says the upper portion of the Tower of Gomor is one of many forbidden places.

Albert Killy is faced with a decision. Fleets are approaching Quent from both the Gilgamesh and the Balarant, and he has to act now if he wants to seize the planet before they arrive. He deploys a contingent of Zwergs to the surface under Arron and Gurran's supervision. They land in Gomor and begin a march across the city, alarming the citizens and defying the city's small security force. From his chamber in the mercenary center, the emissary touches his stone monolith and sends out an emergency signal which is noticed by Chirico and Shako in the deep desert. Shako laments that they cannot reach Gomor in time to be of help. but Chirico has an idea; they turn the stolen Zwerg around and head back into the underground labyrinth.

As Arron and Gurran lead their army toward the upper section of the tower, Chirico and Shako enter the caverns. Chirico fires a random shot into the darkness - and instantly teleports them to Gomor! They strike immediately at the Zwerg army and a firefight begins, which carries inside the tower itself. Again, the air crackles with energy and lashes out at the battling ATs...

"Again! It was happening just as I'd predicted. Where would it transport us to this time? And what had we set into motion?"

Having lost all contact with the Scopedogs chasing Chirico, the combined fleet consider their final option; that of destroying Quent itself.

Chirico smashes the last of his pursuers and nearly collapses from the effort. Finally, Fyana appears in her Berserga and asks him one last time to turn back. He refuses, firing on her and throwing her backward into a teleport field. She is gone. Wiseman congratulates him, and beckons him on by foot.

Chirico struggles to reach the final goal, the central core of the Wiseman bio-computer, the collective consciousness of the Overmen. Chirico lies unable to move, and Wiseman lowers a large machine toward him, one that will complete the bond between God and successor. All Chirico has to do now is stand up...but instead he plays his final gambit, firing a bulled directly into the machine!

At last, Chirico's subterfuge is revealed - having come this far and lead all of his enemies into their own death, he now sets about the work of destroying Wiseman itself. Wiseman pleads with him to stop, explaining that it was he who brought Chirico together with Fyana, and provided her name. This gave Chirico something further to live for, and with life came the desire for strength and power. Wiseman also explains that Chirico need not regret the death and violence he has dealt in the battlefield, saying that "God does not sin when he kills."

Chirico ignores every word, continuing to disable the computer core. As Wiseman's consciousness begins to disintegrate, it lashes out one last time, throwing Chirico to the ground with an electric shock. He rises to see Rochina standing over him. Rochina tries to stop Chirico's sabotage, but Fyana leaps in to overpower him. She recognized his true intentions when he fired only to damage her AT. Together, the two complete the work of killing God and flee to safety as Rochina screams in anger and dispair and what he has lost.

The combined fleets of the Gilgamesh and the Balarant stand witness as Quent explodes with the fury of a sun.

Epilogue: One Year Later

A stolen shuttlecraft soars away from a Gilgamesh planet as a new war dawns on the horizon. Sometime later, a tiny capsule is released into space. Inside this capsule, preparing to disappear into history, Chirico holds Fyana dnd bids farewell to his Friends as they drift off in search of a world untouched by war.

"Coconna. Gotho. Vanilla. Shako. I'm glad I was able to meet all of you. And you, Fyana..."

Chirico Cuvie is reunited with others from the Red Shoulder unit as they pursue their revenge against Yoran Pailsen. Unknown to them, Yoran and his group have created the Perfect Soldier, Ypsilon.