"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."

"For a man like me, who knows only how to fight, combat in Uoodo was something I could not avoid. And within the battle, I met her once more. Now all I can do is try to pursue here. She's tied deeply to my destiny. But what sort of destiny is it?"

Police helicopters comb the edges of the city, firing randomly in search of Chirico and his companions, who now complain that their continued association with him has gotten them into more trouble than they bargained for. Tired of their bickering, he wanders off into the city. Overhearing gossip about a outgoing shipment of jijirium, Chirico ambushes a cop to get more specific information. Coconna, who has been following him, is caught by a rogue member of the Boone Family, who carries her off to the bikers' fortress.

Elsewhere on the planet, Rochina is ordered by Battentain to take a personal role in the tracking of "Program One." Rochina is to take up residence in Uoodo and report directly for there as he obtains information about the secret society and the Prototype.

In Uoodo, Chirico has developed a plan with Vanilla and Gotho to hijack the jijirium shipment. As they make ready, Coconna returns. Frazzled and beaten, she wails that the only way she could escape the bikers with her life was to tell them about the jijirium shipment. Chrico is encourage by this; their involvement should only make things easier for him. And he is proven right - the bikers attack the airfield from which the shipment is to be taken, throwing the entire place into chaos. Using a rebuilt AT with Vanilla providing covering fire from the stolen helicopter, Chirico swiftly makes off with the very truck that was hauling the prize.

"Everything had worked out perfectly. I cared nothing for the jijirium we now had. But if I was right, and it was tied to the Prototype, then perhaps she would come to get it back. Perhaps..."

Proto-One tells Chirico what she knows, but is unable to answer most of his questions about the conspiracy they are both caught up in. When their discussion is interrupted by attacking police, she vows that this time she will fight with him, not against him. Together, they charge into battle.

Iskui is desperate to end this debacle, and Borough gives him the idean to fight fire with fire; they will send in Battling pilots to attack Chirico. While they arrange for this, Chirico makes contact with Gotho, Vanilla, and Coconna. He suggests a rendezvous point and moves out with Proto-One. Seeing the forces arrayed against them, Vanilla tries to back out, but Coconna holds him up with his own pistol. This does the trick.

Inside the tower, Chirico and Proto-One are attacked by the Battling pilots and quickly outnumbered. Proto-One is knocked out of her AT, and Chirico rushes to her rescue, calling a name out of the blue: "Fyana!" He scoops her up and rushes her to safety. She is puzzled by the name, but is glad to accept it as her own. They attempt to escape the tower, but are finally overpowered and separated. Chirico falls to safety just in time to meet up with Gotho and the others, but Fyana is take away by police.

The skies above Uoodo rumble with the sound of approaching airplanes. Scopedog platoons parachute down toward the city. The Melkian army has arrived. But Chirico is concerned only with the woman he has been parted from.

"Fyana...but why did I call her by that name?"

"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."

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?"

Chirico finishes off the first platoon of Balarant Fatties, but a second quickly approaches after a brief exchange of gunfire between Battleship X and the Balarant patrol fleet. Chirico is thrown back into battle, but he is finally overwhelmed and Fyana barely manages to get him back inside after he is wounded.

News of the battle travels quickly to the Balarant HQ Command Satellite. Admiral Zanjeny and his staff review an audio record of the battle, in which Chirico's voice mentions the term "PS." Knowing this to mean Perfect Soldier, Zanjeny orders his patrol fleet to keep close pursuit. On planet Melkia, Rochina reviews puzzling data collected immediately after the battle in Kummen...data which reveals a single ship escaping the palace and being picked up by a larger one. Reports come in of a battle in the nonaggression zone, and Rochina meets with General Battentain for new orders. To Rochina's surprise, Battentain orders him to stand down from the pursuit of the PS; he has taken too long and gotten insufficient results. Rochina turns the table when he drops a hint about the battle going on in the nonaggression zone...and walks away to follow an agenda of his own.

The Balarant now keep their distance from Battleship X, but this gives little comfort to Fyana, who nurses a wounded Chirico and is continuously assaulted by the Red Shoulder video. A seemingly delirious Chirico wanders the flight deck and speaks to an unseen entity, demanding to know why he is being called and where he is to go. Mercifully, he passes out. But no sooner has Fyana gotten him into a cot than the Balarant decide to renew their attack. She prepares to face them alone and Chirico is left behind, unable to get to her aid.

"Fyana...why are you fighting? To protect yourself? To protect me, someone who despises himself? I've been a thoughtless, miserable fool. Why have I been fighting up until now? Who do I go on fighting? Fyana had finally begun to pry open my heart...and I'd slammed it shut again. And once more, almost unconsciously, my heart sought comfort in battle."

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..."

Furious over the turn of events, Lepard is bolstered by the fact that his force outnumbers Rochina's, and when the battle is over, the prize of Quent will go to the Gilgamesh. Rochina relizes Lepard's attempt to recover Fyana was only a ruse, and he pauses to receive visitors; Gotho, Vanilla, and Coconna, who barely made their way through the battle to his ship.

Even Chirico is hard-pressed to emerge alive from this conflict. He makes it back to Rochina's ship with little room to spare. And it is then that Quent makes its move; enormous streams of energy burst our of the Tower of Gomer and blast into space, destroying everything in their path! Both fleets are devastated, and the only survivors are Rochina, Chirico, Fyana, Gotho, Vanilla, and Coconna, who manage to escape in a shuttle and power down to avoid being hit.

They are soon picked up by the only other ship now in Quent orbit - that of the Secret Society. Killy gloats over his victory, with all of his enemies now under his control and the secrets of Quent ripe for the picking. But before he can act, his ship is seized by an invisible force and pulled away from the planet by the same superior intelligence that has manipulated everything leading to this moment.

Chirico finally recognizes its identity.

"Wiseman. The name of Quent's mysterious, ancient intelligence. As we proceeded into the unknown, toward our destinies, I felt as if the fate of everything we knew now rested with us."

"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."