"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?"

The Phantom Lady meditates in police HQ and is approached by Borough, who demands that she prepare to go into battle once more. She refuses. Borough angrily overrides her, freezing her with the name "Proto-One."

The police roll into the Battlig AT hanger, and a Scopedog appears to challenge them. The exchange is devastating, but brief - and the AT is demolished. The police open it up, but Chirico is not inside. Behind them, another Scopedog emerges; and this time it's the real thing! Chirico lets them have it full force, blowing them to bits and escaping into the streets to do more damage. His companions follow with still another Scopedog for later use.

In police HQ, The Phantom Lady is subjected to a mind probe to investigate her erratic behavior. Borough and Iskui are shocked at what they find. Her initial memory from awakening on Lido reveals that Chirico was the very first human being she ever saw. Iskui presumes that she had been contaminated and will no longer follow orders - but Borough insists that she must be made to kill Chirico in order to break the mental connection. Iskui reluctantly agrees.

Rochina and his spy network watch with interest as Chirico makes his way toward police HQ. He burns out his Red Shoulder Custom and moves to his other Scopedog, which takes him directly into the police tower. There, The Phantom Lady waits for him in her Brutishdog...but this time Chirico gets the upper hand and takes her captive. Rochina learns of this and dispatches the news to Battentain. Now that Chirico has made contact with the Prototype, it is time for the Melkian army to move in.

As the police regroup outside the tower, Chirico finally speaks to The Phantom Lady. She admits that she does not want to kill him, and he asks her - her name. "Proto-One" is all she can answer.

"The woman who had changed my destiny was not longer an enemy. I couldn't shake the feeling that I was sinking deeper and deeper into quicksand. But at the same time, I felt something amazing. Never before in my life had I wanted so much to keep on living."

"Months have passed since Uoodo was consumed in fire. I've now wandered into civil war-torn Kummen. Mercenaries. Front lines. How appropriate for me. But now I know that she is here as well. It has to be her. But why?"

Chirico attempts to communicate with the pilot of the Blue AT, but his Marshdog is demolished and he is thrown clear. Kan Yu and his troops arrive, and the Blue At vanishes. later, Chirico reports his findings to Gon Nu - the pilot of the Blue AT is definitely a Perfect Soldier.

At the Fan tom Club, Coconna sings Chrico a love song she has written while Vanilla introduces some of the other mercenaries to him, Bully Kiderra and Pol Potaria. Quick action from Chirico saves the club from a guerrilla's attempt to plant a bomb, earning him the respect of the other men. That night, Chirico works on Gotho's personal computer to write a mission disc for his AT that will positively identify the maneuvers of a perfect Soldier.

The next morning, Chirico joins Potaria and Kiderra on a mission under Kan Yu's command; a supply boat needs an AT escort through guerrilla territory. Also joining them is the imposing Quentman, Ru Shako. They don't have to wait long for action - enemy Turtles launch an attack from the banks of the river, and Kan Yu's group quickly engages them. Chirico spots the Blue AT again and puts the mission disc to work. Their battle is short, but reveals much.

"My anti-PS program had worked. A little more work, and we'd be evenly matched. She must know it's me. But then why is she doing this?"

At a Melkian army base, Gon Nu prepares to return to EX-10. With him is Rochina, who is looking forward to seeing Chirico again.

Meanwhile, Chirico and his companions rush into Nitan and launch their counterattack on the invading Turtles. Chirico looks around for Ypsilon, but the PS is not participating in this fight. He is insted watching from the palace as reports roll in. He protects when Kanjelman orders a retreat, but is overruled. Ypsilon complains to Fyana, who admits that she has become afraid to fight in any further battles.

At Niitan, Chirico's group takes out a few more enemies, and Kan Yu finally appears with the rest of the mercenaries to drive the invaders back into the jungle. The next morning, Niitan lies in ruins. Vanilla broods over the loss of the Fantom Club, depressed over losing his purpose in life. Gotho approaches to announce winds of change.

Chirico reports to Gon Nu on the events of the previous evening and receives a full pardon, even though he defied Kan Yu. Bitter and humiliated, kan Yu leaves...and Chirico is introduced to Rochina. He has come to discuss the Perfect Soldier situation. Back at Kanjelman's palace, Fyana has undergone an examination to determine why she has developed a fear of fighting. To Ypsilon's outrage, Borough declares that the interference of Chirico is what has poisoned her mind.

Rochina describes how Proto-One was created, but is shocked to learn that a second PS is in action. Since Chirico has more experience than anyone,he will be sent into darkest Kummen to recover Proto-One. A short time later, a special task force under Kan Yu prepares to depart into the jungle. Once again, it includes Potaria, Kiderra, and Shako. Chirico is along as a specialist. having decided to sign up with the army, Vanilla desperately wants to join them...but arrives too late to leave with Chirico.

Coconna sits sadly on the dock as Chirico's boat disappears into the distance, and she sings her love song one last time...

"It's okay baby. I guess I'm just used to it now. you never used to say much, but we have time 'til dawn. You never really treated me that well, but I could see a little bit of the real you inside. So long, baby. I loved you once upon a time."

Chirico and Fyana travel the jungle together in his Marshydog, and when the two are ambushed by Veela ATs, three unexpected allies come to the rescue: Kiderra, Potaria, and Shako. Afterward, Chirico tells them what happened to Kan Yu and introduces Fyana, the PS they have been tracking all this time. Potaria and Kiderra agree to accompany them on their mission to assault Kanjelman's palace, but Shako dissents; he is bound by his contract with EX-10 and cannot bring himself to violate orders.

A short while later, an EX-10 helicopter passes overhead and spots the rogue mercenaries. Gon Nu relays the news to Rochina, who orders him to keep Chirico under observation. His actions could give them the opportunity they need to launch an all-out attack on the palace.

with Fyana's help, Chirico and the others destroy another platoon of Turtles and make their way closer to their objective. At the palace, Albert Killy informs Borough and Ypsilon that he is sending a new AT for Ypsilon to fight in now that his Snapping Turtle is gone.

Chirico's group reaches one of Kanjelman's arsenals. Fyana makes her way up to it alone and finds herself a Brutishdog. The others make short work of the installation. Fyana informs them of something she has overheard on the radio; that Kanjelman has ordered all Veela Guerrilla units back to the palace. Potaria is confused by this news, unable to figure out why the prince is abandoning his tactics after all this time.

Heading back into the jungle, Chrico and the others are spotted by another helicopter from EX-10, which is piloted by Vanilla. He reports that he has found Chirico, but is ordered to return to base. Chirico watches him leave and realizes that many eyes are now on him. His next move must be a decisive one.

"Go Nu wasn't going to let me go. As the enemy closed in from both sides, my excitement built. But in the palace beneath the gathering storm clouds, a deep whirlpool of suspicions was also building..."

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."

Huge vehicles watch the approaching transport truck and prepare to launch an attack. But they are unprepared for a skilled AT pilot in a Scopedog, who swiftly disables one of their vehicles. The struggle is interrupted by a voice from above; a ship passes overhead and calls out to the AT pilot. An astonished Chirico realizes it is Bouleuse Gotho!

In orbit around Sunsa, the Teltain has escaped its battle with the Balarant, and Futtor makes plans to continue the pursuit of Chirico and Proto-One. Meanwhile, Ypsilon examines data from Battleship X. To his disbelief, Chirico seems to have recovered from his earlier injuries three times faster than any normal human...

Gotho's vessel drifts over Sunsa. Inside, Chirico and Fyana are introduced to their attackers: Zophie and her gang, who salvage weapons from the desert for Gotho to sell off world. They travel to Zophie's fortress, within the airtight ruins of a damaged building. Vanilla and Coconna are there, and react to their arrival with mixed emotions. Vanilla is ecstatic, but Coconna is furious when she sees Fyana for the first time. Chirico says nothing.

Later, Zophie approaches a weeping Coconna, who reveals that as a Red Shoulder, Chirico has always been cold and unemotional. Meanwhile, Gotho berates Chirico for acting this way toward Coconna. Fyana argues for Chirico's sake, but stops herself before she can say too much. The scene is broken by the arrival of Ypsilon and a platoon of Tortoises from the Teltain. Setting up a perimeter around the fortress, they demand that Chirico be surrendered. Gotho prepares to answer with gunfire, but Zophie stops him - Chirico, after all, is one of the Red Shoulder devils who destroyed their planet, and she is more than willing to throw him to the wolves.

Chirico prepares to face Ypsilon alone, refusing even Fyana's help. She begins to wonder if he really is as cold and unfeeling as Gotho said.

"I know best how I should fight. Gotho had called me a war machine. A murder machine. And now so had my beloved Fyana. If I really was a machine, I doubt their words would hurt me as much as they did. But I'm just a man, and my battle is this hell continues...as does my crushed existence."

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?"