"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."

"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."

No longer able to travel the river route to Kanjelman's palace, Kan Yu's task force is airlifted to nearby Crescent Moon lake, from which they will travel by land. A Veela spy watches the airlift and reports to Kanjelman. The news quickly passes to Borough, who informs Ypsilon that Chirico is on his way...and he plans to take advantage of their next battle in a way that will end the confusion in Proto-One's mind.

The airlift of Kan Yu's task force is interrupted by Veela artillery. Vanilla plays the unwilling bait in his helicopter while the ATs drop into the jungle and eliminate their attackers. Word of this also reaches Kanjelman's palace, confirming the whereabouts of the task force. Borough and Ypsilon contact Albert Killy to propose their plan: Proto-One will be made to watch as Ypsilon kills Chirico in an ambush, thus ending her distraction.

Some time later, Kan Yu's men cross Crescent Moon lake with a gunboat escort. Abruptly, one of the gunboats is struck from beneath; Ypsilon and a platoon f Turtles launches an ambush from their hiding place under the water! Chirico and the others engage the Turtles in their own ATs, and Ypsilon singles out Chirico immediately. As they face off, a helicopter flies overhead. Inside is Borough, who forces Fyana to watch the scene below.

She tries in vain to avert her eyes as Chirico's Marshydog takes heavy damage...and when it is finally too much for her, she lunges for the helicopter's flight stick, spinning it out of control! The careening helicopter knocks Ypsilon aside and crashes headlong into the shoreline. Chirico watches the crash from his slowly sinking AT.

"In Ypsilon, I had seen an almost bottomless hatred for me. And yet, I saw something else, she'd risked her life for me. Fyana. An indescribable warmth filled my body..."

"Fyana...the last thing I remember was escaping the jungles of Kummen with Fyana. There's no doubt about that. But afterward, something took us..."

Chirico and Fyana wake up in the shuttle they used to escape Melkia. It has inexplicably come to rest inside the hanger deck of some large facility. They investigate their whereabouts and discover themselves to be on a gigantic space battleship, heading toward an unknown destination on auto-pilot. Left with no way of stopping it, the two finally have a quiet moment, in which Fyana is amused to learn that Chirico has never tasted alcohol before.

The peace is interrupted by blasting music, which comes from a self-playing video that depicts Chirico's notorious Red Shoulder Battalion slaughtering civilians during the war. Like the ship they are on, it is automatic - and try as he might, Chirico is unable to stop the nightmarish pictures. This drives a new and unexpected wedge between Chirico and Fyana. The shame he feels for his past is matched by her forgiveness and understanding... but neither of them knows how to give voice to their feelings.

Suddenly, an alarm sounds - their ship approaches a Balarant patrol fleet, and a platoon of Balarant ATs rockets toward them from the distance. Chirico rushes to one of the ship's Scopedogs and plunges into battle, desperate for a diversion from his inner turmoil.

"What else could I do? I knew what would happen if the Balarant captured a PS. Besides, I'm a Red Shoulder, a man born to fight. The only place I feel at home is in battle. Fyana and I had escaped the jungle to find a new world. And here I was, forced to confront old wounds. Trapped in an unknown ship, headed God knows where, having to fight the Balarant. And the woman I loved, who I was fighting to protect, seemed to be drifting farther away with each passing second."

Arron and Gurran monitor Ypsilon's emotional index from the Teltain. Now that he faces Chirico, his readings have levelled out to those of a proper killing machine. ypsilon and Chirico lunge at each other, and Fyana holds off the Tortoises, admonishing Chirico to rember that they're both fighting to live. He instructs her to get back inside and stand ready in the control room. Carefully, Chirico lures Ypsilon and his troops toward the engines of the crashed ship and leaps off the edge. Ypsilon follows - and Fyana activates the thrusters! Caught in the backblast, Ypsilon's Strikedog is smashed, and the invaders retreat.

Now convinced that a third, more aggressive party has joined the fight in the nonagression zone, Zanjeny and his staff order a task force into the area in support of their patrol fleet. On board Teltain, Ypsilon recovers from his injuries and thinks of his next battle with Chirico.

Knowing Ypsilon will be back, Chirico tampers with the verniers on the now-silent hull of Battleship X and finally realizes what planet he is on: Sunsa, the site of the bloodiest battle of the Hundred Years War...a battle he himself has remembered in nightmares. An AT landing craft appears, and Chirico and Fyana rush to the control room as it lands on the hull. Out steps Ypsilon in another Strikedog, with more Tortoises backing him up. One by one, the verniers blast away at them.

Ypsilon reports this setback to Futtor on the Teltain, who suddenly has to face a problem of his own - Balarant ships approach, and he has no AT platoon to fight them off! Forced to tip his hand, Futtor goes on the offensive, and a devastating battle erupts in space! Having found their way inside Battleship X, Ypsilon and his remaining men reach the empty control room, and discover that Chirico has set the entire ship to self-destruct! They escape just in time, and launch as the vessel rips itself apart.

chirico and Fyana has also gotten away, loading a transport truck with ATs and driving deep into the Sunsa desert. There, others await them...

"Would we ever have any peace? I felt like screaming. If there was a God on this world, he was a cruel one. Too cruel. This planet's name is Sunsa. And I know it holds no welcome for me at all..."

On the Teltain, Futtor insists that they must leave Sunsa now that Ypsilon has been recovered. Arron and Gurran reply that their mission take precedent. Ypsilon must be allowed to fight Chirico again, and they must stay to observe.

On Rochina's ship, Chirico fine-tunes a Scopedog and writes himself a new mission disc containing everything he knows about the maneuvers of a PS. Fyana speaks with Chirico, admitting she is afraid for him, but he counsels her to accept what must happen. Ypsilon is fighting out of loneliness, and will not stop until one of the tem is dead. Ypsilon, meanwhile, renews himself with a jijirium bath and launches for the surface in a new Strikedog.

On the other side of the galaxy, Melkian General Karmeny meets with Battentain to discuss the implications of what has happened in the Nonaggression Zone. Battentain is shocked to learn of Rochina's defection, and admits he never quite knew how to read the man. Despite the risk to the peace treaty, a task force of Gilgamesh battleships must be sent to Sunsa with Rochina as their target.

Chirico crosses the Sunsa desert to Siguray Crater, where Ypsilon's empty landing craft stands waiting. Chirico takes the bait, and the battle is joined! This time there are no distractions; the two clash with each other time and again. Chirico's mission disc works perfectly, allowing him to match Ypsilon move for move. Rochina takes notice and finally announces to Fyana what he has suspected all along: that Chirico is a true Perfect Soldier! And at long last, Chrico fires the fatal shot that takes Ypsilon down!

Before he can finish Ypsilon off, however, Chirico is interrupted by Fyana, who gives him the shock of his life - that he is more than human. Chirico insists that his mission disc is what allowed him to win, but then notices that the disc burned itself out only a few minutes into the fight. From then on, it was his own ability. Ypsilon insists in his final moments that Chirico has to be a PS...Ypsilon's pride would not allow him to die at the hands of a normal man.

Later, Chirico prepares to leave Sunsa, Rochina's words echoing through his mind: "You are a PS. You want proof? Then go to planet Quent. There you will learn everything."

"What was it that lay hidden in my past? I'd fought Ypsilon and won. But I couldn't believe it. There was no way I could be a PS. The Planet Quent...what awaited me there?"

Killy watches from his ship as the Gilgamesh fleet approaches Quent, where Rochina's Balarant fleet awaits them. Arron and Gurran report from the surface that they are safe, but their entire AT army was destroyed. Killy is content to wait and watch history repeat itself now that the power of Quent is reawakening.

Admiral Lepard speaks with General Battentain, who warns him about what he is walking into. Someone has been tampering with the secrets of this planet, perhaps even the lost Perfect Soldier.

Arron and Gurran watch as Lepard lands and is greeted by Rochina. The two officers begin their verbal fencing, Lepard demanding that the Prototype be returned. Rochina attempts subterfuge, but when Gotho, Vanilla, and Coconna appear, his lies about losing contact with Chirico and the Prototype are revealed. Recovering, he offers to rendezvous in orbit and bring the Prototype with him. Everyone who watches the proceedings know what a risk this will be...especially with Chirico involved.

Chirico infiltrates Rochina's AT platoon, and the Balarant fleet lifts off into space to play its part in the deadly game. Rochina's landing party docks with Lepard's ship, and he produces Fyana, insisting that the Gilgamesh now leave Quent. Lepard refuses, but as a Scopedog steps forward to seize Fyana, Chirico makes his move, striking out from inside a Balarant Fatty. Rochina escapes with Fyana, and the Battle quickly escalates into an all-out bloodbath!

Chirico takes a moment to free Gotho and the others, then escapes outside into the escalating firefight.

"The battling had turned more intense than I expected. And then somewhere in my body, I felt it. A premonition. Yes, one from the darkness, for only me to know. And that's when the whole horrible thing happened..."

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..."