"The armistice which finally ended the Hundred Years War was signed right around the time I deserted the Melkian army. That was six months ago. I had slipped away from the military's eyes...and lost myself in the crowds in the city of Uoodo."

A Melkian satellite tracks the progress of Chirico (now called "Program K"), as he enters the sinister Uoodo City. Mere moments later, he is caught by a gang of bikers who toss him into a truck along with other victims, and roar away to evade the Uoodo Security Police. Taken to the bikers' fortress on the outskirts of the city, Chirico and the other slaves are forced to dig for jijirium in the ruins of a computer factory.

Later that night, the police pay a call on the fortress. Uoodo's chief of police has come to inform the gangleader, Boone, that their arrangement must be dissolved - now that the war no longer serves as a distraction, he can no longer turn a blind eye to the slave raids. Boone attempts to bribe him with even more riches, but a sudden slave uprising takes all of them by surprise. Grabbing a motorcycle during the confusion, Chirico escapes back into Uoodo, chased by bikers. The Melkian spy network intervenes, and Chirico falls into a scrap yard. He climbs into the wreck of a Scopedog, the only shelter he can trust.

"It was a place that held a familiar scent for me. With only the cold feel of metal on my hands, a once-dead warmth now glowed to new life inside me. And, feeling as safe as a child held to its mother's breast, before I knew it I was fast asleep."

"Since deserting the army, the war ended, and I found myself in the city of Uoodo. Now I have the city's police force trying to kill me. But why? I've done nothing to have earned these constant attacks."

The police step up their assault on Chirico, and he abandons his now-damaged AT to escape with Gotho and the others. They hide out at Vanilla's home to plan their next move. Gotho tries to convince Chirico that his future is in Battling, but Chirico is too full of questions. He slips away, overpowers a street cop, and sneaks into the police tower wearing a stolen uniform. He makes it all the way to Iskui's office and holds the man at gunpoint, demanding to know why he has been hunted ever since Lido. Iskui agrees to take Chirico to a place where his questions will be answered, and the two leave in a private helicopter to the heliport outside Uoodo.

Meanwhile, gotho and the others have found an abandoned underground subway, and are making their way to the same location in order to scout for information that can help Chirico. They make it inside just as Iskui springs a trap. Chirico is surrounded, but Gotho provides him with a diversion from the control room and he evades capture. meeting up with his rescuers again, Chirico blunders into another room deep inside the base - The Phantom Lady's living quarters. He boldly approaches her, recognizing her as the same woman he saw on Lido. She flees before Chirico can ask her any questions, and police troops pick up his trail again. Vanilla manages to hijack a helicopter, and flies his friends to freedom.

"It was her. Was that really the Prototype? But what is she?"

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..."

On the outskirts of EX-10, a small force of guerrillas knocks out the guards and ambushes the sleeping base. The mercenaries respond quickly, and Potaria arrives just in time to spot a woman fleeing into the jungle. Potaria broods about it later in the Fantom Club. The woman's name is Monica, and they were childhood friends.

The next day, Kan Yu chooses a task force to join him in an attempt to locate the guerrillas, who are believed to be hiding in Zonmu village. The task force includes Chirico, Kiderra, Potaria, and Shako. They arrive at Zonmu some time later, and Kan Yu orders all the villagers brought forward for questioning. The villagers deny any connection with the guerrillas, but Kan Yu orders the village searched. The search turns up Monica.

she refuses to reveal anything about her fellow guerrillas, even when forced by Kan Yu to play a cruel game of Russian Roulette. Chirico intervenes, and Turtles erupt for hiding! A firefight ensures which carries into the nearby mountains. Once again, the Blue At appears and Chirico attempts to communicate with the pilot. Separated from the battle, Chirico gets out of his AT and approaches his opponent on foot. The Blue AT opens its cockpit, revealing that the pilot is not Fyana after all - it is another Perfect Soldier altogether, a wiry young man who knows Chirico's name!

Surviving the helicopter crash, Borough crawls free in time to watch Fyana rise and flee into the jungle. Underwater, Chirico swims free of his sunken Marshdog and fires handgun rounds into the air tanks of Ypsilon's snapping Turtle. Ypsilon has no choice but to abandon the fight and loses himself on shore as the rest of Kan Yu's task force finishes off their remaining enemies.

Injured and angry, Borough is flown back to the palace, where he asks Kanjelman to order his men to hunt down the treacherous Proto-One and shoot her on sight. Both Perfect Soldiers have failed him, so Kanjelman declares that this is the last favor he will grant. Back at the lake, Chirico repairs his Marshydog and sets off to find Fyana, defying Kan Yu's orders to stop. The others die with Chirico, and their mission to find the Prototype PS gets underway again.

Not far away, Fyana picks her way across a mountainside, when suddenly she runs into the Blue AT. She tries to run, but Ypsilon stops her. She grabs his pistol and threatens to shoot, but he doesn't believe she can. They are interrupted by gunfire from another Turtle, who declares that he has orders to kill her. Ypsilon mounts up and leaps to Fyana's defense - but cannot bring himself to fire on his own allies.

Chirico notices the firing from nearby and leads his companions to Fyana's aid, just as Ypsilon's AT is disabled by the other Turtle pilots. After rescuing Fyana, Chirico frees Ypsilon from the wreckage of his AT, and Ypsilon slinks away in defeat. But when Chirico turns around, Fyana is gone - and so is Kan Yu. Kan Yu chases down and captures her, determined to take her back alone and abandon the others in the jungle.

Chirico tracks Kan Yu down and fights him hand to hand for Fyana's life. They wrestle each other into a raging river and Kan Yu is swept away. Fyana pulls Chirico free of the raging water and saves his life. the next morning, the two finally share a quiet moment together in the sun. But their peace cannot last while their enemies still live...and Chirico is determined to bring this fight to an end.

"I'd finally found Fyana again. Why did I still need to fight? Was there any point to my trying to stop Borough and his group?"

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."

As Chirico and his friends go to work patching up derelict vehicles, a familiar face looks down on Sunsa from orbit: Rochina. Now in command of a Leslion-class Balarant Battleship, he has crossed both the nonagresssion zone and his allegiance to Melkia in order to find Chirico again. Rochina's ship descend on the abandoned supply station, and Chirico's group is quickly overwhelmed and taken captive. Chirico is taken directly to Rochina, who offers the release of his friends if Chirico will consent to face Ypsilon again. Chirico questions Rochina about who he really is. Rochina's only answer is that he is a man from the kingdom of heaven.

Captain Futtor discusses the situation with Arron and Gurran aboard the Teltain. They have not heard from Ypsilon since the raid on Zophie's fortress, but they are sure he will go after Chirico despite the Balarant presence. When that happens, the Secret Society must be ready to recover him.

Chirico agrees to Rochina's terms, and is freed to prepare for the battle. He doesn't have long to wait - Ypsilon and his small platoon launch an attack on the Balarant landing party and fight their way quickly inside the perimeter. Rochina orders all ships to launch, and Chirico is left behind in a Fatty to face his enemy. In short order, they find each other in an empty chamber deep inside the supply station. Once again, they draw their weapons and prepare to engage. Rochina arrives to watch with Fyana in tow, but there is nothing that can be done to stop the fight now.

"His will to fight was practically a madness. But, as opposed to him, my heart didn't burn. the thing that drove me on was an almost pitiful craving for battle that raged within me."

Arron and Gurran have tracked Chirico's progress and speculate about following him themselves. Killy agrees to let them go, provide they use extreme caution.

Chirico and Shako enter the Quentian village, but rather than talking with the chief, Shako instead gives Chirico a drink which causes him to pass out. That night, the women of Shako's tribe perform a strange ritual. Chirico wakes afterward, and Shako explains that they wanted to determine if he was "one who was changed," but says no more.

Rochina prepares to leave the Sunsa system, and Fyana demands to know what he thinks Chirico will find on Quent. Rochina doesn't know precisely, but he does admit to having been following the orders of a higher mind...and has questions of his own to be answered on Quent.

The next morning, Chirico questions Tedaya, the chief of Shako's tribe. Tedaya explains that Chirico might be "one who was changed," but says that he must speak with Meji to learn more. Venturing deep into an underground labyrinth, they find Meji, who appears more ancient than the very rocks around him. Meji explains something of Quent history, about beings who appeared 3,000 years ago and where driven away into darkness after they said all Quentians would be reborn by their hands.

More confused than ever, Chirico later runs into Arron and Gurran, who chase Chirico and Shako deeper into the caverns...which give way to ancient underground technology. They corner Chirico and fire a tranquilizer dart at him. The air around them comes alive with power, and everything begins to fade away...

"Even as consciousness faded from me, I saw it. Saw how they'd disappeared. What had happened? And what was going to happen to me? Was I still even alive?"

"It seemed that Killy, Rochina, and I were three of a kind. The ship we were on, under Wiseman's control traveled on through the darkness of space, its destination still unknown to us."

Killy's ship proceeds through a belt of sinister floating tubes and toward a gigantic artificial planet, which he calls the technology of God. Drawn inside, the ship is set down and a silent command is spoken to Killy; to bring Chirico to Wiseman. Rochina admits to having received the same commands in the past, and Killy orders him imprisoned.

As Killy leaves with Chirico, the time of execution has finally come for the other prisoners. Ever the trickster, Vanilla manages to overcome his would-be executioner and frees the others. Rochina is allowed to escape with them, but is not trusted with a weapon.

On planet Melkia, a report of the disaster at Quent reaches Battentain. One Gilgamesh ship avoided destruction, and sighted the Secret Society ship leaving intact. Battentain postulates that since the Gilgamesh and Balarant both lost ships in the conflict, they now have the basis for an alliance against the mysterious enemy on Quent.

While Killy and Chirico march closer to Wiseman, Rochina fills in his fellow escapees on what brought him this far, and warns them that Chirico is far more than they imagined him to be. The group is sudenly caught between two groups of Killy's guards, and a running battle begins, from which Rochina manages to slip away.

Finally, Killy and Chirico reach the center of the complex, and Chirico is levitate into the core shaft. There, the truth is finally revealed; he is a natural-born PS, a new "Overman," for whom Wiseman has been waiting all this time. Chirico is to be his successor, the master of the entire Astrigius Galaxy. Offered this blessing, Chirico accepts it.

An incredulous Albert Killy is told that his mission is over - and he is killed by Wiseman without a second thought.

"I was Wiseman's successor. His will had determined this forme. I could finally se my destiny unfolding before me. Because I was a child of God."