The episode begins with a view of the Neo sapien fleet stationed between the moon and Earth. Soon after a closeup on North America the scene shifts to nighttime in Phaeton City (formerly Chicago), and then into the sewers beneath the city.
There are a number of Neos and an e-frame standing guard. Going past are Lucullus and Phaeton, who is in a powered wheelchair and wears the suit designed to help reduce the symptoms of Auto Mutation Syndrome. Phaeton tells Lucullus, "Once the Terran Resistance used these tunnels, now they are mine. Here, Lucullus, you will build my final retreat." Lucullus offers, "Phaeton, there are other locations more easily defended. A fortress in the mountains, perhaps." An anger is present in Phaeton's voice as he firmly states, "I will not leave my capital! My new command post will be here, under the streets of Phaeton City! My city!" Lucullus is still hesitant, saying, "But, construction of such a facility would require cutting off power and essential services to the Terrans in the city." Phaeton stops his wheelchair, turns his head to look at Lucullus as though he is an idiot and asks, "Do you think I care for their suffering?" Lucullus tries to defend himself with, "I... I was merely thinking of the effect on the Terran workers. We... we need them to..." "There must be no Terrans in Phaeton City!" shouts Phaeton. Lucullus is taken aback, "But... but the current Terran population numbers over three million!" And in a matter-of-fact voice Phaeton just says, "Then remove them."
Phaeton once again begins moving, but Lucullus does not continue to walk with him. Livia enters and stands at attention as Phaeton approaches her. She tells him, "Marsh has escaped from New York City." He responds coldly, "My other Generals would be afraid to tell me of such a failure. That is why I let you live." For a moment she is obviously taken by fear, but she regains her composure as she starts saying, "He... he will probably attempt to join the other ExoFleet e-frame. The one piloted by the traitor Marsala." Almost in a mocking tone Phaeton asks, "You will capture him this time, won't you, Livia?" She responds, "Yes. A trap has already been set for Marsh, he will not remain free for long." Phaeton says ominously, "For your own sake I hope you are correct."
J.T. Marsh is flying along the coast of Maine when he gets a warning that his fusion battery is running low on power (he borrowed the battery last episode after losing his fusion pack), and he notes that he doesn't have enough power for weapons. He lands at the rendezvous point (another bit from the last ep) and exits his e-frame yelling Marsala's name. Turner walks out of the forest and asks him, "You the weapons technician?" Marsh tells him, "No, Felson was in the other e-frame... should've gotten here last night." Turner replies, "Well it didn't. They didn't show." Marsh quickly reacts, "They? How'd you know the other e-frame was a two-seater?" and rushes Turner before he can get a shot off. As they struggle, Marsh demands, "Where's Marsala and Felson! You set us up, didn't you?" Turner (who apparently didn't think to note that Marsh mentioned two names, Marsala's and Felson's) cries out, "Help me, he knows!"
At that a number of Neo e-frames emerge from the surrounding woodland. One fires a shot at Marsh, but J.T. saw it coming and dodged, so it hits Turner instead. Marsh gets off a couple of shots with his hand blaster, but they don't do any damage. He runs underneath a large Neo frame as shots are fired in his general direction. Marsh runs as more shots go past, and he apparently trips over a fallen tree trunk. It is hollow, so Marsh crawls inside, where he sees a rabbit also cowering. Marsh jokingly apologizes to the rabbit about dropping in. When the foot of one of the Neo e-frames crushes one end of the trunk, the rabbit runs out. The Neo reacts to the movement and fires seven shots, all of which miss. "Hmph. Filthy Terran vermin" mutters the pilot, and the Neo frames move on. Marsh then exits and runs back the way he came.
Back at the clearing, a Neo pilot (drawn like Thrax, but with a much different voice) approaches Turner's unconscious body. "Useless Terran. You'll pay for your incompetence," he says as he picks him up and places him in the pincers of another e-frame before ordering that pilot to have him removed. As he is about to enter his own e-frame, Marsh takes aim and shoots him, knocking him back. Marsh then runs to the Neo e-frame, gets in, and orders the cyberjack to activate and reconfigure. He then picks up his own e-frame and flies off.
It is still night, and the scene is a Neo sapien complex at Niagara Falls. Galba and Gracchus approach a Neo on duty and Gracchus tells him, "The Ministry of Genetics wants the body of the captured Neo sapien traitor." The Neo goes and pulls out the shelf with Marsala's body inside. Galba and Gracchus stand nearby and Galba states, "His name was Marsala."
They then leave and fly to Maniton Island. Inside what appears to be a cabin, Marsala's body is lying on a table. Lucullus is heard saying, "He certainly appears dead." Galba tells him, "The injection I gave him produces a most convincing simulation." "Convincing enough to keep him from falling into the hands of Livia," adds Gracchus. Galba walks over to Marsala's body with an injection gun in hand, saying, "And now this injection will revive him." He gives him the injection, but nothing happens. "Well..." asks Lucullus. Galba is confused and says, "I... I don't understand, it should have restored him to consciousness immediately." Suddenly Marsala's eyes open and Gracchus realizes, "It did!" Marsala grabs Galba by the chin and tosses him into Gracchus and they both land on Lucullus. Lucullus cries out, "Stop him! Guards!" The guards are Neo megas, and they turn to see Marsala rush straight into them, knocking away their weapons and knocking one down. The other attempts to subdue him from behind, but Marsala quickly flips him into a pile of firewood.
Marsala runs toward a wooden dock, as someone is heard to shout, "This way!" Before Marsala can get to the jet-ski at the end of the dock it is hit by a blast and explodes.
Galba asks, "Marsala, do you want peace between Terrans and Neo sapiens? Please, listen to me." He signals the others to leave the two of them alone, and they do. "It is obvious the Neo sapiens are losing the war. Some of us went to Phaeton, to persuade him that he must make peace with the Terrans. Those Neo megas are no longer alive." he says bowing his head. Marsala tells him, "Phaeton will continue the war until the last Neo sapien has fallen." Galba knows this, saying, "There can never be peace while Phaeton remains in command. We brought you here because we need your assistance. We want you to kidnap Phaeton."
Back in Phaeton City, the Resistance member known as Picasso runs through a dark alley. Coming upon a poster of Phaeton, he sprays it with something that causes the picture to morph back and forth between Phaeton's face and one that is disfigured and sticking out its tongue. The noise of a nearby cat startles him enough that he drops his can of spray paint. He picks up the cat, shows off his artwork, and when the cat hisses at the picture of Phaeton, Picasso says, "Guess you're on our side," and takes him along to join the resistance. As he tucks him into his jacket Picasso says, "Well welcome to the cause, soldier. Your first duty will be, uhm, rat patrol!"
A blast is heard and as some Neo e-frames walk nearby Picasso says with worry in his voice, "Uh- oh, these guys are really tough critics." He heads down the alley, but flattens himself against the wall of a building when a Neo frame pauses its patrol to glance down the side street. Once the e- frame continues on, Picasso does as well. He stops when he sees Terrans moving out of a building single file under Neo guard. "They're rounding up Terrans, but why?" he asks aloud. He starts to head back down in the direction he came, but soon sees a Neo searchlight coming from a intersecting street. "They're all over the place." Soon he pries the lid off of a sewer and goes down into it, the cat still with him. As the Neos walk overhead, dust and small bits of concrete are shaken loose from the sewer ceiling. He says to the cat, "Guess we outsmarted 'em. Don't worry, they'll never find us down here."
Just then a large Neo e-frame smashes through a sewer wall, and Picasso dashes behind some rocks. He watches as the Neo frame walks past. Soon entering from the hole made by the e-frame are Phaeton (in his hoverchair), Livia, and two guards walking behind. Livia tells him, "Construction is proceeding ahead of schedule." Phaeton is still not pleased, asking, "But where is Lucullus? He should be supervising this project personally." Livia tries to excuse him, "His duties are many, Phaeton." Phaeton ponders "Yes... perhaps too many." And the group then heads down a different tunnel, this time using an exit the original architects put there. Picasso tells the cat they need to inform Napier, and he runs off.
Back on Maniton Island Lucullus explains the plan to Marsala. "Phaeton has become obsessed with the construction of an impregnable bunker under Phaeton City. He spends much of his time there, overseeing every detail." Gracchus continues, "If we strike before it is completed, Phaeton will be ours." Marsala is skeptical, "The tunnels and sewers beneath the city will be heavily guarded." Galba voice holds optimism as he tells him, "Yes, but we have your e-frame with its special cloaking ability." Unconvinced, Marsala says, "That would improve the odds. Still, how am I to find Phaeton in that underground labyrinth?" Lucullus tells him, "Hmm... I can arrange for him to be in the main chamber." Once again Gracchus finishes the thought, "You can wait nearby, render him unconscious, and take him away in your e-frame." Marsala is still unhappy with the situation and he asks, "Why don't you enlist the aid of the Terran Resistance? They must know the tunnels better than anyone." Gracchus replies, "The Resistance would never trust us." Marsala responds, "I am not certain I trust you." Lucullus fires back, pointing an accusing finger, "If it weren't for us you would be awaiting execution in Phaeton's prison." Marsala stares at him. Galba tries to calm down both sides, pushing down Lucullus' arm and saying, "Marsala, we have a common goal. Peace, and survival for all of us; Neo megas, Terrans, and Neo sapiens. Will you help us?" Marsala thinks for a moment before responding, "I will."
At Resistance Headquarters, Peter Tanaka sits at the radar screen that detects and incoming e- frame. He warns Voodoo, who is on watch outside with a pair of binoculars. "I see it. One e- frame... no, no, two! A Neo sapien and... it's carrying an ExoFleet e-frame!" The various members of the Resistance pull out their weapons and prepare for a fight. The Neo e-frame lands, drops Marsh's frame, and the cockpit opens. When Sean Napier sees it is Marsh inside he yells to his troops, "Hold your fire!" Then to Marsh he says, "J.T.! You might've let us known you were coming." Marsh responds, "I didn't have much choice. Can we talk? In private?" Napier nods and Jinx Madison and Eve Hanley leave his sides, though they don't look happy (either for getting left out or because when Marsh arrives it usually means trouble for them). Motioning to the old barn behind him Napier says, "Step into my office."
Inside Marsh says, "Turner's a traitor, working for the Neos." "Turner? Are you sure?" Napier asks in disbelief. "He helped the Neos set a trap. Marsala and Felson were captured... or worse," says Marsh, dropping his head with a depressed look. Napier asks, "Where's Turner now?" Marsh tells him, "The Neos have him. They don't forgive failure." Napier walks up to Marsh and puts a hand on his shoulder trying to console him, "I'm sorry about Marsala. He was a good soldier." Marsh says, "Yeah, and he's my friend."
Just then Tanaka enters and knocks on a wooden ladder to let them know he's there. "Got a message from Picasso. There's a big, ugly rat in the sewer and we should send in the exterminators." Napier asks, "Does this rat have a name?" Through clenched teeth Tanaka says, "Yeah. Phaeton."
Next we see Napier jacking into his e-frame. "Thought you were a politician now, not a soldier." Marsh says jokingly. Napier smiles, "For a chance at Phaeton I'll come out of retirement."
Back on Maniton Island, Marsala is preparing to leave. Galba tells him, "Well, your e-frame is fully repaired and powered. You still doubt our sincerity?" "Perhaps." With some sadness in his voice and on his face Galba says, "You are under no constraints. You can, if you choose, fly to the Resistance. Or back to ExoFleet." Marsala tries to cheer him up, "That would not end the war." Marsala then climbs into his e-frame and takes off.
In the sewers of Phaeton City, the Resistance is on the move. They proceed down one that is almost completely filled with water (or a blue/purple sewage). "Is this one of your secret shortcuts into the city?" Marsh asks. Napier tells him, "Yeah, just hope the Neos still don't know about it." Going single file, in order, are Napier, Marsh, Hanley, Tanaka, Voodoo, and Madison.
Marsala has arrived in Phaeton City, and with his cloaking device active nonchalantly glides by some Neo e-frames. He enters a tunnel and continues, cloaked.
In the central chamber beneath Phaeton City, Lucullus approaches Livia and asks, "Livia, where is Phaeton?" Phaeton, now in his e-frame, enters and says a bit menacingly, "I am here." Lucullus and Gracchus approach him and the former tells him, "We believe we should stop making Neo sapien warriors and create more Neo megas instead." Phaeton stares at him while Gracchus explains, "It is new technology that will win the war, not brute strength." Phaeton simply states, "I do not trust the Neo megas." Lucullus seems somewhat surprised and saddened as he responds, "But the Neo megas have served you loyally." With a voice that begins with wonder and ends in rage Phaeton replies, "Have they? Tell me Lucullus, what have you done with the body of the Neo sapien traitor Marsala?!" and Phaeton once again has an insane expression on his face. Off to the side Livia smiles.
Just then the Resistance blasts a nearby tunnel wall, burst in, and begin to battle with some Neo e-frames. Phaeton tells the two Neo megas, "I'll deal with your treachery later!" and he goes off to fight the intruders. Livia is still nearby, with a look of satisfaction on her face.
Phaeton proceeds down one of the tunnels, and Marsala decloaks once he has walked past and begins to follow. He then opens fire, missing about a half dozen times before scoring a number of hits as Phaeton turns to face his attacker. As Phaeton turns his back to him as though to flee, Marsala continues his barrage, hitting Phaeton almost continuously while he already buckles in pain. Still in pain Phaeton struggles to regain control, falls forward after more hits to his back, but he manages to crawl into a side tunnel. Marsala follows, but Phaeton shoots an overhead pipe that lets out a constant stream of water. Marsala fires blindly as his e-frame walks through the wall of water, and once past it Marsala is somewhat surprised to see that Phaeton has abandoned his e-frame near the entrance to a smaller sewer. Marsala exits his frame, grabs his blaster out of its holster, checks to the right, then left, then right again before proceeding into the sewer himself.
Back in the central chamber Livia tells the two Neo megas, "You will not succeed in your treason." Lucullus seems stunned, "We... we had no part in this attack." Grinning, Livia says, "You two will be the first Neo megas to inhabit our newly completed dungeon." As she begins to pull out her communications device she continues, "The guards will show it to you. Ahhh!" Lucullus knocks the device out of her hand, and Gracchus pulls out a gun, quickly saying, "Do not move!" Livia states, "I am second in command to Phaeton. You would not dare harm me. Not while Phaeton is free." Lucullus tells her, "Phaeton will be unable to help you." Taken aback, Livia only word is, "What?" Lucullus goes on, "His guards will be shocked to discover that you have conspired with the Terran Resistance to assassinate Phaeton." Livia has regained her composure and says, "No one will believe you." Lucullus coldly tells her, "You will be in no position to dispute it." And he pulls out his own gun.
Meanwhile, Phaeton has struggled to a dead end. There is only a wall and a six inch pipe with water trickling out of it. From behind him he hears, "Phaeton! There is nowhere for you to run." He looks back to see Marsala standing at the tunnel's entrance. Phaeton says, "So it is you, Marsala. We have come full circle my brood brother. But now I am the one betrayed." Coming down to face him, Marsala tells him, "You betrayed your own cause. Your way was never right. But surrender and your life will be spared." "I have no life!" Phaeton yells back, shaking his fist, his hand losing cohesion and oozing through the bandages. Marsala seems to be pleading with him, "Don't make the same mistake I made fifty years ago. Don't waste more Neo sapien lives in a hopeless fight." As Marsala says this, Phaeton looks at his oozing hand and then at the small pipe. "Noooo! You will not take me!" Phaeton shouts, firing his blaster and forcing Marsala to duck behind a corner. Phaeton then sheds some parts of his Auto Mutation Syndrome suit and Marsala starts to look and see if he can leave his cover to shoot back, when Phaeton fires and continues firing with a blaster attaches to his left arm. As he fires, he holds his right arm up to the small pipe's opening and his entire body slowly begins to go through it.
Lucullus, Gracchus, and Livia are still continuing their conversation. Livia says angrily, "Betrayers! Seizing power to make peace with the Terrans." Lucullus counters, "Peace? There can never be peace between a superior race and an inferior one. Those who think so are fools." Not understanding, Livia asks, "Then why?" Lucullus tells her, "Phaeton is insane. Neo sapiens can never defeat the Terrans under his leadership." Gracchus explains, "Neo megas are superior to both races. Just as Neo sapiens must dominate Terrans, we must lead the Neo sapiens." Lucullus pulls out a communicator and says, "This is Lucullus. I order the immediate arrest of the traitor Galba."
With the shooting having since stopped, Marsala makes his way to where Phaeton had stood as the last part of Phaeton enters the pipe. He sees the empty components of Phaeton's suit and holds his ear to the pipe, where a gurgling sound is heard. "Phaeton..." he says under his breath before he runs off.
The next view is of a number of Neo e-frames charging and firing constantly. The Resistance flees under this barrage, but Tanaka turns to fire a spinning circular saw blade that slices off the leg of an amphibious frame, which splashes into the water and (for some reason) explodes. More Neo e- frames continues to rush through and Napier shouts, "They're gaining on us! We won't make the exit!" Just then part of the tunnel wall explodes, knocking over an e-frame. It is Marsala, and he fires two missiles at the ceiling that bring large sections of concrete down on the pursuing Neos. "Marsala!" says Marsh in disbelief. Napier says, "Thanks for the help." Marsala responds with a thumbs up.
Lucullus is speaking to a gathering of a number of guards and e-frames in the central chamber. Livia stands, bound and gagged. "The Terran attackers have escaped thanks to the treachery of Livia. We have no time to mourn Phaeton. We must purge the traitors who conspired against him. Gracchus has a list of those who cannot be trusted." Phaeton pushes apart two Neo e-frames with the arms of his own, to make an entrance that stuns everyone there. Pointing the e-frame arm at the Neo megas he says, "I assume your name is at the top of the list, Lucullus." After a moment two e-frames proceed to carry away the two Neo megas, whose faces convey both shock and fear. Pointing to Livia, Phaeton demands, "Release her! The Neo megas are traitors! I will destroy them all, and create new ones to take their place." Livia tells him, "The Neo mega Galba was arrested by Lucullus. He, at least, is loyal." Smiling, Phaeton says, "Then Galba alone shall be spared." The Auto Mutation Syndrome overtakes Phaeton, however, as his face convulses and his body liquifies and spills out of his e-frame. He tells Livia, "This e-frame needs repair. See to it!" Obviously disgusted she replies, "Yes, Phaeton." And she is further mortified when he oozes by her feet.
Back at the Resistance Headquarters, the sky is blue and Marsh and Marsala look at the scenery. Marsh asks, "Do you believe the Neo megas really want peace?" Marsala replies, "I believe Galba is sincere. Of Lucullus and Gracchus, I am not sure. But we all agree on one thing: Phaeton will never surrender. He wants to be destroyed. If he can, he will take this entire world with him."