"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."

Sleep in Vanilla's home is broken by the sound of thunder. Police units have begun to literally take the city apart to find them, and before they know it they are boxed in with no escape! Vanilla, Gotho and Coconna despair for their lives until Chirico snaps them back to attention and leads them through an impossible route to safety. Having lost everything, they refuse to go on, but Chirico does not expect them to, in any case.

Iskui and Borough receives reports from their assault units, who report that Chirico's hideout has been destroyed, and now they ponder wheat to do with their troubled "Prototype." On the streets below, Chirico makes his way into the AT hanger of a Battling arena and goes to work on a Scopedog. Gotho and his companions prepare to leave Uoodo through the underground tunnels when Coconna demands that they turn back to help Chrico. Gotho and Vanilla are typically reluctant, so she turns back on her own. She follows Chirico's trail to the arena, and Vanilla appears in the nick of time to save her from being caught by a guard.

Reunited once again, the three find Chirico inside, building a Scopedog into a heavily augmented Red Shoulder style AT. This is when Gotho makes the connection - Chirico was once a Red Shoulder, one of the deadliest AT pilots in the war. No sooner have they agreed to aid him in his continuing battle, that the police arrive and prepare to move in. Chirico takes cover, ready to return their brutality in kind.

"They could never understand the pain of being a Red Shoulder. Thinking that, I prepared to meet the advancing energy. Only by fighting could I forget the horrors I'd seen. I fought on only so I wouldn't remember. But someday..."

"I had managed to escape the police...but hadn't been able to take the Prototype with me. I didn't even notice the airborne AT units drifting down like snow."

Iskui and Borough watch helplessly as the police tower is surrounded by Melkian Scopedogs. Rochina leads the assaul force, demanding that they give themselves up. Instead, they call Albert Killy, who orders Iskui to wait for the backup he is sending. Borough is to escape to the heliport with Proto-One.

Rochina barks the orders to move in, and all hell breaks loose. Chirico and his companions discover this, and Chirico explains to them what he has learned, namely that all these events have centered around the Prototype, who is an experimental Perfect Soldier created by the Melkian army. Chrico was just a pawn in the Lido raid, and it has made him a fugitive.

Iskui is killed as Rochina's men enter the police tower, but the Prototype is nowhere to be found. Overhearing their radio transmissions, Chirico deduces that she has gone to the heliport and he intends to follow her there via the abandoned subway. He locates her, and asks her to escape with him. She cannot, claiming that if she tries to leave her captors, she will die.

Finally, time runs out. Rochina's army attacks the heliport and are met by a new enemy: Tortoise-type ATs sent by the Secret Society to cover the escape of Borough and the Prototype. The entire base, like Uoodo itself, collapses in flames. Chirico walks through the inferno alone, cut off from everyone he now holds dear.

"The city of Uoodo was disappearing. Vanilla...Gotho...Coconna...Fyana...please don't leave me to be alone. Where are you? Where have you all gone?"

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."

"So many villagers killed. caught in the midst of the war. The stench I smelled seemed full of the anguish of the dead."

Travelling by boat toward the inner reaches of Kummen, Chirico and the others try to keep a low profile; no easy task with the hot-tempered Kan Yu in charge. Against Chirico's batter judgment, Kan Yu stops another boat that passes by, insisting it must be searched for Veela weapons. The search turns up nothing...but when kan Yu fires a cannon at the boat, explosives hidden within it rip across the water. Kan Yu gloats that Veela Guerrillas cannot be underestimated.

Later, the boat reaches Ramoh Temple, a religious colony that is supposed to be neutral. Again, Kan Yu insists that the platoon march in with their ATs to look for enemies. Exasperated, Chirico agrees, and reluctantly follows the others into the huge compound. Nothing turns up until Kan Yu spots a boat similar to the one he blew up earlier. he repeats his action, and gets the same result - it also carries Veela weaponry.

Their cover blown, Veela Guerrillas burst out of hiding and open fire on Kan Yu's task force. The battle is joined and quickly ends...but now the secrecy of the mission has been compromised, and they must ask for new orders from EX-10. Those orders are delivered a short time later by a helicopter pilot new to the EX-10 ranks: Vanilla! Chirico wanders the wreckage of the temple, pondering this turn of events.

"What is it that leads men to the battlefield? For some, they pull the trigger to earn their daily bread. For others, the chance to fight for their ideals. For me, I can't live without the scent of gunpowder and death. This was no longer a house of God. It was now merely a pile of rubble."

High above planet Melkia, Albert Killy listens to Arron and Gurran, two scientists studying the PS, speculating on what must be happening in the civil war below.

Holding Borough at gunpoint, Chirico questions him. Ypsilon arrives, but cannot intervene. Borough explains that the Secret Society brought the PSs here to try and perfect them; their emotions have proven too erratic, and have constantly interfered with their efficiency as killing machines. What's more, they can never be remade into normal human beings. Kiderra attempts to attack Ypsilon from behind, but fails at the cost of his own life. His move disrupts the scene, giving Ypsilon the chance to attack Chirico. Fyana can only watch from her AT as the two grapple and fall from level to level down into the bottomless mineshaft.

Outside the palace, Gon Nu gives the order to move in. Behind them, a third party prepares to enter the fray: the Melkian army. Lead by Rochina, their orders are to overwhelm the palace and destroy everyone in their way. Only the PS Prototype is need alive. Unaware of this new development, Vanilla finds Potaria, who passes along the key given to him by Kanjelman.

Chirico and Ypsilon land at the bottom of the mineshaft, which is full of oil and priceless jijirium. Both their ATs have been damaged, so Ypsilon leaps out and challenges Chirico to a hand-to-hand fight. Fyana appears in her Brutishdog, and when Ypsilon refuses to stop, she fires on him. He is furious at her final betrayal, but the scene is broken by the laughter of Gon Nu. Peering down from above, he proclaims victory. Now that Chirico is of no further use. Gon Nu will destroy him along with everything else.

Rochina, however, has already begun bombing the palace from outside. Suddenly, Gon Nu himself has become expendable! Chirico and Fyana escape as the palace begins to crumble, and Ypsilon is left standing alone as Borough dies in the fire.

Chirico and Fyana find Vanilla, who gives them Potaria's key. It will activate an escape shuttle, and Vanilla wants them to flee in it. At the last moment, however, the insufferable Kan Yu appears and prepares to finish Chirico off once and for all. Shako intervenes, having finally decided his commanding officer isn't worth following any more.

Their enemies now dealt with, Chirico and Fyana launch in the shuttle, just in time to evade Melkian Scopedogs. They burst out of the palace and into the open air, their future opening up before them.

"My journey through Kummen was at an end. For my own sake, I had chosen to enter hell. For Fyana's sake, I was now leaving it behind. Love? could it be even I was capable of fighting for love?"

Zanjeny and his crew debate the continuing situation. Space Battleship X cannot be identified as a Gilgamesh ship, but the Balarant still cannot risk starting an incident in the nonaggression zone. All they can do is wait for their opponent to make the first move. On the ship, Fyana has come to a decision - she will surrender herself to the Balarant in exchange for medical treatment for Chirico. Her attempt to do so is observed by Futtor's men, and just as Fyana seems to have won, the Balarant ship is destroyed by the Teltain.

She makes it back safely to Battleship X, and as the unknown planet looms closer, the Teltain launches another attack. Fyana attempts to radio Ypsilon, begging him to stop the assault, but communication is knocked out before anything can come of it. The ship begins to descent into the atmosphere of the planet, and a platoon of MKII Tortoises is launched against Fyana. Ypsilon joins the attack in his Strikedog, but when he faces off against her directly, his emotions begin to cloud his judgment.

Despite this, he manages to capture her, and as his men haul her away, Teltain launches another barrage of missiles at the descending battleship. Horrified, Fyana tears herself away and plummets to Chirico's aid once again. She dives inside, followed by more Tortoises, but everyone is thrown into chaos when the giant ship finally smashes into the surface of the planet and comes to rest. Just as Fyana is finally cornered, Chirico rushes to her aid in a Scopedog of his own, and fights his way out to the surface of the smoking ship...where Ypsilon awaits. The sun of the unknown planet rises as they level their weapons at each other.

"My strength had returned to me. But, as strong as Ypsilon's murderous rage was, the smell of blood from this planet's past was even stronger."

"I was searching for any oxygen canisters left in the wreckage. I'd realized that I had miscalculated. My oxygen was running out. My initial calculations had let me to believe that I could just reach that unmanned supply situation. But I'd sacrificed one more canister than I'd counted on. Zophie's presence was the reason."

Chirico has made the magnanimous gesture of giving Zophie one of his own air tanks, but now regrets it as his own nears its limit. Evading Balarant patrols, Chirico eventually finds an underground supply depot, and sets Fyana down to investigate it. Inside, he finds more air tanks, but gives up his bazooka to carry them. He returns to Fyana and resumes his walk...but Zophie intervenes, having grabbed and armed the bazooka! Before she can end it all, however, other come to Chirico's rescue - Gotho, Vanilla, and Coconna charge over the dunes in a salvaged buggy, and scoop everyone up just in time to avoid another Balarant patrol.

The patrol chases them into the very supply station Chirico was bound for, and he takes over the buggy to face off against the single Fatty AT that pursues them. Destroying the Fatty, he rushes to Fyana, and prepares a liquid jijirium bath to save her from the edge of death. As he does this, Gotho and the others deal with Zophie...and Coconna emerges as the unlikely victor. Unleashing the pent-up anger of a lifetime, she pummels Zophie with everything she has, including the heart-rending truth that she, too, lost her family in the war.

As Fyana's life is restored, Gotho and Vanilla inform Chirico that Zophie has gone...but she left no forgiveness behind.

" I never answered her charges. Even if I had told her the truth, that my unit wasn't on this world when her family was killed, I still would have only been making meaningless excuses. Because I'd done the same thing in other places. Even if she knew the truth, she wouldn't forgive me. And in my heart, I felt the same way."

Chirico Cuvie wakes up in the Sandrunner of a curious little man named Gecko, who scolds him for trying to cross the Quent desert alone on foot. Chirico looks out the window of the vehicle in the desert traders' caravan; they are approaching the Tower of Gomor.

In orbit around Quent, Albert Killy cautions Arron and Gurran, who are about to embark on an expedition. Chrico is not the only threat to them; the planet itself can take lives.

Chirico parts with Gecko in Gomer and heads for the mercenary center, where he demands to speak with a Quentman. The workers in the center react with suspicion, and a chase erupts when Chirico becomes the target of security guards. He finds his way into a room that houses the emissary to the Quentmen. Chirico asks questions about Quent and the PS, but the emissary cannot provide answers, saying instead that he will get Chirico some help.

Chirico flees the mercenary center into the hands of Hazegar, a thug-for-hire who insists that Chirico come to meet his master. Gecko intervenes, telling Chirico to surrender for moment. He resists being picked up, but is shot with a tranquilizer and taken to the spaceport where Arron and Gurran await to take custody. At the last moment, fate intervenes in the form of the Mayor of Gomor, who claims Chirico is the guest of a Quentman, whose authority must be obeyed. The Quentman turns out to be Ru Shako, recently returned from Kummen!

Amazed, Chirico prepares to embark on his quent into the desert with his unexpected ally.

"Our reunion on Quent could only be called miraculous. With uncertainty and anticipation mixing within me, I stepped forward into an unknown world. what awaited me at the end of this desert?"

Gotho, Vanilla, Coconna, and Fyana trek across the Quent desert. Coconna screams at Vanilla for not landing their escape shuttle closer to Gomor, and he insists that only an expert pilot could have gotten them this far. Shako appears, and though they are overjoyed to see him, he is not reassured. He explains that a child of God will soon descend to Quent and decide the fate of the Universe.

On the Secret Society ship, Chirico has uncovered treachery; Arron sabotaged their trajectory in order to delay the arival at Quent. Chirico kills him, leaving Gurran in despair. Rochina, who has stowed away on the ship, watches and waits. Later, Chirico descends alone to the Quent surface witha a new AT. Gurran resists the urge to shoot him down in cold blood, resigned that Wiseman is now in control of all their fates.

Gotho and the other assemble an old Berserga AT for Fyana and discuss what is to come next. Shako spots Chirico's ship descending and goes to meet him in Gomor. Chirico disembarks in his own AT, the Rabidlydog, and is greeted by Shako. Chirico explains that he will need the destructive power of Gomor to meet the approaching fleet, and Shako offers to take him to the control center. There, they examine the machinery and Chirico explains to Shako the cold truth behind what is happening; although the ancient Quentians tried to exile the Overmen, their final creation now lies beneath the very feet of the modern Quentians. It has used war to manipulate history for 3,000 years. Now Chirico, the ultimate product of that war, will take control of it from here on.

Shako tries to stop him and succeeds in damaging the equipment, but is overpowered and shot by Chirico. Gotho and the others, having trailed after them, burst in and open fire. Chirico slips away and plunges into the desert in the Rabidly dog. Furious, the others watch him disappear, and Fyana prepares to give chase. Chirico radios Gurran, ordering him to assemble their AT troops near the site of the Quentian villge now that the Tower of Gomor is out of commission. Fyana calls to Chirico to stop, but he rejects her and insists that she leave this planet far behind.

"My final battle was beginning. Would I be blown to atoms...or would I inherit the throne of God?"

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.

Chirico finds his beloved Fiana held hostage by Bararant in an experimental facility near Koba City, and he and his comrades have to fight their way in to save her.

Chirico Cuvie has been assigned to a new unit, the Red Shoulder division. His selection is not an accident, as he has an ability that possibly makes him the ultimate soldier. The Red Shoulder unit is callous and merciless in their training, and will test Chirico's ability to the limit.

Decades ago, two people took drastic measures to ensure their escape from a galaxy engulfed by war. Unfortunately, the past has finally caught up to them.

Chirico doesn’t care what Titania wants nor that the COMPLANT is falling apart around them. Fyana is the only person who matters and Chirico won’t stop until he gets her back.