Wolf Bronski pilots the Admiral's shuttle, which he used to retrieve the Jumptroops of Charlie Company, over the Maryland-Pennsylvania border. The instrumentation in front of him lights up and starts beeping as a Neo e-frame comes up behind them, takes aim, and then fires a missile at them. The missile strikes the rear of the shuttle causing it to burst into flames. The jumptroopers inside are rocked, and smoke causes a couple of the jumptroopers out of their armor to start coughing. Bronski reports that the engine was hit, and they're going to have to crash land.
In Canada, at Great Slave Lake, Marsh, Marsala and Algernon search for the secret Neo base at which they believe Phaeton had his doomsday device constructed. Algernon assures them that the particle accelerator was shipped there by hover train. He says that they should find the base by following the spur line, and Marsala notices that there is one under the surface of the water. They follow it and find a Neo base.
The e-frames land nearby, Marsh contacts the rest of the squad, and they each exit. Marsh and Marsala hope that they've found the right base and can get to the doomsday device in time. Algernon notes the beauty of the sunrise. Marsh looks at the sunset and says, "If we're wrong the sun may never rise on the Earth again." Algernon remarks, "The sun is always rising somewhere. After all, our darkness means light to the other side of the world." Marsh responds, "Heh. You almost sound optimistic, professor. How would a doomsday device work?" Algernon replies, "If I were going to destroy the Earth, and I had as little imagination as Phaeton, I'd simply blow it up."
At Battle Creek, Michigan the battle between a group of Neo tanks and the resistance with their captured tanks has done heavy damage to the area. The resistance is receiving help from orbit, with the Resolute II firing at the area. Above the planet, a single Neo e-frame is seen making a kamikaze run at the Resolute II, but is destroyed before it can do much harm. Back at Battle Creek, Sean Napier surveys the area. Satisfied with the situation, he reports to the Resolute II that they can stop firing. He then orders the group to proceed.
Inside Phaeton's bunker, Livia reports that the resistance armored column has broken through, and is on its way to Phaeton City. Phaeton says, "I will destroy them all." Livia is frustrated, asking, "How? Our forces are crumbling." Phaeton says again, with more resolve, "I will destroy them all." Livia then asks to bring all Neo forces back to Phaeton City to make a stand that may be their only chance. Phaeton says, "Do as you wish. It does not matter."
On the deck of the Neo base at Manaus, Brazil, Medusa reports to Thrax that Livia wishes to speak with him. When he wonders why, she says, "Perhaps she wishes to reassess your leadership capabilities." "Perhaps," says Thrax in a tone that can mean he doesn't think so, or doesn't care, as he walks inside.
Inside, Livia asks Thrax if there have been any attacks in his sector. He says, "Negative. Apparently we aren't considered important enough to attack." Livia tells him, "You are to abandon the Amazon and bring all troops under your command to Phaeton City." Thrax states, "I have very few troops under my command." Livia reiterates, "I don't care how many troops you have, I want them all in Phaeton City. The order is direct from Phaeton." Thrax tells her, "I can no longer obey Phaeton's orders. When the Terrans reach this place I will surrender myself and the troops under my command." Angered, Livia says, "Coward! Remember what happened to the last traitor in command of the Amazon." Unfazed, Thrax replies, "Do you imagine that I'm afraid of you?" Livia then orders, "Medusa, deal with this traitor!" Medusa pulls out her blaster to attack Thrax, but he knocks her down with little difficulty. She fires at him from the ground, but he quickly ducks, draws his weapon, and fires, rendering her unconscious. He addresses Livia once more, "I don't know what purpose there is to our lives, but I have decided to preserve as many of them as possible. Even Medusa's, she's only stunned. Thrax out."
Enraged, Livia leaves the room. She goes to Phaeton, and reports about Thrax's traitorousness. "Thrax is a traitor." Phaeton asks, "Who?" Livia explains that it was he who took command after the last Draconis clone was executed. Phaeton muses, "Was he really the last? I wonder." Livia states that many of the officers must be disloyal, since otherwise the ExoFleet would've been defeated long ago. Phaeton decides to send Neo warriors and Neo lords to remove all Neo officers, and have them brought to Phaeton City. This is obviously a far more drastic step than Livia intended, as she wonders who will lead the troops. Phaeton tells her to follow him.
They go into a room that is filled with more clones of Shiva, Draconis, and Typhonus. Phaeton activates one of each. He tells them that they were his greatest generals, but that each failed him. They are being given one last chance, but must first prove themselves. "There is one Terran I hate more than any other. He must perish alone, destroyed by my own hand. Go, and bring me J.T. Marsh." They leave to do his bidding.
Back at Manaus, Telemachus tells Thrax that e-frames are approaching, but he cannot identify them. Thrax gives instructions to all of those under his command to take to the rain forest. He says that special orders from Phaeton are for them to join him in a guerilla war, if possible. But if something happens to Phaeton, they must surrender. "Remember, it is Phaeton's wish that if the war is lost, you should live," he announces. Telemachus then reports that the e-frames have identified themselves as Neos. Thrax dismisses it as a Terran trick, and tells Telemachus to go quickly. Telemachus does not wish to leave, but Thrax tells him, "Once on the planet Mercury a commander ordered me away from a hopeless battle. Perhaps he saved my life so that I could save yours. The others are in your care now, Telemachus. You must all survive, no matter what happens. Now go, that's an order." Telemachus grudgingly obeys, and he salutes Thrax as he exits.
As his troops take to the rain forest, Thrax goes to his e-frame, removing a tarp that covered it. "Well, my friend, we have one last fight." Thrax enters, the cyberjack connects, and he takes off. Closing on the Manaus base are eleven Neo e-frames, perhaps more, flying in formation. Thrax succeeds in destroying three of them. The leader, a Neo lord, recognizes that it is Thrax, and tells him, "Your time is up, traitor." Thrax responds as he dodges his shots, "Phaeton is the traitor. He betrayed all Neo sapiens." As he says this, he comes around and shoots down the leader. After crashing and exiting his e-frame the Neo lord remarks about Thrax's weakness being that he relies on machines to fight. He flies and is able to clip Thrax's frame, knocking him off balance long enough for a few of the others to target Thrax and score a couple hits. Thrax crashes in the river, exits his frame, and tries to swim away. But an amphibious frame captures him, and the Neo lord orders him taken to Phaeton City.
The Neo lord flies to the Manaus base, and frees Medusa, who was locked in the food locker. He tells her that she is in command of the Amazon now, and she will carry out Livia's orders and send the troops to Phaeton City. She says, "Of course... I... I will obey." "Of course, you have no choice," says the Neo lord. She starts to make an announcement for the troops to prepare for an evacuation to Phaeton City. She is interrupted when she hears some noises outside, goes to look and sees Ketzer's followers climbing up the side of the ship. She goes to exit, but Ketzer is waiting for her and he injects her with something.
Back at Phaeton's bunker, he is telling his generals that Marsh is a favorite of Winfield, is the best e-frame commander in the ExoFleet, and that the ExoFleet now knows of the doomsday device. Livia is shocked at the thought of a doomsday device, and Phaeton says, "Now you see why I do not fear the Terrans." Phaeton goes on to say that because of the aforementioned reasons he expects that Winfield will send Marsh to destroy the doomsday device, and so they will be able to find Marsh at the base where the doomsday device was constructed, at the Great Slave Lake.
At the Great Slave Lake, Marsh is giving orders to his squad, saying that they will first disable the command and communications center and then secure the doomsday device, at which point the professor will take over. The take off, and begin firing on the base, a couple different types of Neo warriors come out to meet them. Marsh blasts open the cover to a sewer drain, and the squad enters. The squad proceeds in the main tunnel, and they split up into different ones.
In one that is half-filled with water, a point is reached where Maggie Weston believes they can go no farther. Just then they come under attack from a Neo warriors. One of the crab types comes up out of the water to surprise Weston, but Nara Burns blasts it. In a different tunnel a lizard type drops down onto Yuri Stavrogan while another gets hold of him. Marsh blasts the one holding Stavrogan while the other spits acid on his windshield. As it is about to spit again, Marsh blasts it. Stavrogan thanks J.T., who remarks that he'd hate to lose his old wingman so close to the end.
Meanwhile Marsala and Algernon have gotten to the particle accelerator. Algernon reports to Marsh, "This base was built to create antimatter. A few grams would level a city, a million times that may have been created in this complex." Marsh asks, "Is there any danger of the antimatter being detonated?" Algernon replies, "A great deal of danger. You see, the antimatter is no longer here."
Later, inside that part of the complex, Algernon explains to Marsh that antimatter can only be stored in a magnetic field, like the one that is there. He states that detonating antimatter is quite simple, as it is only a matter of bringing into contact with normal matter. Marsh wonders where it is, and Marsala notes that Phaeton probably has it close to him, as it would be comforting.
In Phaeton's bunker, Phaeton pushes a lever that brings the doomsday device out into the open with much cackling electricity. Livia congratulates him, and says, "With antimatter we can order the Terrans to withdraw or see the Earth destroyed." Phaeton grips her head in his e-frame's pincers, much to her surprise, saying, "An ultimatum? No, Livia, you do not understand. The Terrans cannot be trusted. I am going to destroy the Earth, as Mars was destroyed." Livia asks, "But... but what about the future, the... the Neo sapien order?" Phaeton lets go and walks away, saying, "I have automutation syndrome, what do I care about the future?" Livia has a look of helplessness and shock on her face as she gazes up at the doomsday device.
Marsala helps Algernon back into the rear seat of his e-frame. Marsh orders the squad to regroup outside. Once outside Marsh reports to Winfield that the antimatter is no longer there, and they suspect it has been moved to Phaeton City. He is interrupted as the group comes under attack and it looks as though a pair of ExoFleet e-frames are destroyed. Marsh orders Marsala to take Algernon back to the Resolute, and he exits the battle with a terrified Algernon in the back seat. Marsh is being approached by the Neo generals, and they exchange fire before Marsh flies off with them trailing him. Weston and Rita Torres are in the air back-to-back, and later shoulder-to shoulder as they each track a Neo frame and destroy it. Torres gives Weston a thumbs up.
Meanwhile Marsh is targeting Shiva, but gets hit in the back himself. Still under fire Marsh dodges and takes out two Neo frames. He takes to the woods and through a canyon, but is pursued by a Neo lord in an e-frame. The Neo lord fires two missiles, but Marsh meets them with two of his own. On one of Marsh's dodges the Neo lord is faced with Kaz Takagi in front of him, and gets shot out of the sky.
Two Neo Y-wings target Nara, and each fires two missiles at her. She shoots the four missiles and then destroys the two Y-wings. Suddenly she gasps in pain, and her eyes begin to take on a green glow. She comes under attack gets caught by Shiva, and Stavrogan goes after her. Marsh tries to provide cover, and Stavrogan scores a few hits on Shiva's frame. But Shiva swings around and launches a missile that hits Stavrogan squarely in the front and sends him flying back and crashing into the water. Trapped in his e-frame, he tries to open the emergency release to his cockpit, but it doesn't open.
Marsh notices Stavrogan's crash. He tells Nara to take the squad back to the Resolute, and he'll go after Yuri. Kaz objects, since Stavrogan is also his friend, and Marsh relents. Marsh lands and is met by more Neo frames, whose shots knock him down. Takagi destroys one, drives off another but takes a hit from Shiva. Shiva then uses his frame to hold Marsh's down and remove its fusion pak, which he proceeds to destroy. His e-frame powerless, Marsh is helpless as Shiva picks him up and takes off.
Kaz, having since crash landed, sees Marsh get taken and runs over to Yuri's frame yelling about them needing to help J.T. Once he gets there, however, and looks into the cockpit and stops. He crouches down, and while on the verge of tears reaches through a hole in the windshield and switches back the emergency escape latch so that it stops beeping. He gets back up, and slowly walks away.
Later, the three generals have returned with Marsh. They throw him down, and he looks up to see Phaeton saying, "J.T. Marsh... welcome to Phaeton City."