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The shuttle carrying Charlie Company is shot down. The battle at Battle Creek between the resistance e-frames and captured tanks and a group of Neo tanks ends, with the resistance victorious. Livia orders Thrax to bring all of his troops from the Amazon to Phaeton City for a final stand, but he tells her that he intends to save as many Neo lives as possible, and plans to surrender to the ExoFleet. This prompts Phaeton to issue orders for a purge of all officers by the Neo lords. Seeing e-frames approaching, Thrax orders all his troops into the jungle. Once Thrax is captured and taken away, Ketzer attacks the Neo base and with only Medusa there has little trouble injecting her with something. Able Squad locates the complex where Phaeton's doomsday device was constructed, but finds that it is now gone. As they leave they are ambushed, and in the course of the battle Stavrogan is killed and Marsh captured. Marsh is then taken to Phaeton City and brought before Phaeton.

Able Squad and Charlie Company land in Washington D.C. to attack a Neo lord breeding facility. Bronski gets shot down, but is able to escape his e-frame and join Marsala in his. Winfield then recalls Able Squad, and wants them to depart immediately despite Marsh's objection that the jumptroops won't have proper cover. On the Resolute II Winfield tells them that he is sending them to locate Phaeton's doomsday device, and Algernon will go with them to determine the best way to destroy it. Bronski, with no e-frame, remains behind. Meanwhile Praetorius has prematurely released all his Neo lords, so they have no wings and lack intelligence. But they cause immense trouble for the jumptroops, destroying their evac shuttle and forcing them to withdraw. Winfield lets Bronski take his personal shuttle to get them out, and he arrives just as it appeared as though the jumptroops last stand at the Washington Monument would fail.

ExoFleet jumptroops and e-frames land on the moon in an attempt to retake it from the Neo sapiens. But when Phaeton sends nearly every e-frame on Earth after the fleet itself, the e-frames invading the moon are recalled. DeLeon receives permission from Marsh to stay on the moon with the jumptroops to help them. Battles rage both on the moon and above it. DeLeon and O'Reilly battle Typhonus and kill him, but Alec is mortally wounded in the process. Before he dies he has O'Reilly help him use the black box from Typhonus' e-frame to appear to be Typhonus in a transmission to Phaeton, in which he tells him the Neo pilots are either surrendering or retreating. As punishment for such betrayal, Phaeton activates the self-destruct mechanism on all the Neo e-frames. The combination of this and Alec, as Typhonus, telling the Neo troops on the moon to surrender ends the battle. Afterwards, with Alec DeLeon dead, O'Reilly delivers DeLeon's e-frame black box to Maggie Weston.

A mission to deliver explosives to Earth Resistance lands Bronski and Takagi in Alaska, where they meet up with the Chicago resistance. They must place the explosives on a train so that the base to which it is going will be destroyed. But when they discover some of the cars carry many of the world's greatest art creations, Hanley hesitates. So they steal the cars with the art, plant the explosives in the particle accelerator, and get the empty cars destroyed so the Neos will stop looking for them. The rest of the train makes it to Great Slave Lake in Canada, where it explodes the next day.

Phaeton has Shiva take most of what remains of the Neo sapien fleets to Venus in a final attempt to destroy the ExoFleet. With the Resolute II undergoing repairs, Admiral Winfield takes a large portion of the fleet towards Earth in an attempt to fool the Neo sapiens into thinking an attack is immenent, and therefore withdraw to defend Earth. Shiva calls Winfield's bluff, and proceeds with an attack on the fleet at Venus. An e-frame assault on the Neo fleet fails, but a followup by torpedo boats inflicts heavy damages on the Neo fleet. Shiva then personally leads an e-frame assault, but is shot down and dies as the attack fails.

Galba pretends, for the sake of Praetorius, to conjecture that the ExoTrooper they have captured is in fact Marsh masquerading as Takagi to avoid being taken to Phaeton (which is true because he told Marsh to). Praetorius has the Neo lord spare Marsh's life and taken to his cell. When Marsh is about to be taken to Phaeton, Galba helps him escape and get to Kaz's exofighter. He then contacts Able Squad, which is able to locate his position and proceeds to, along with Jumptroop Company Charlie, attack the brood complex. Marsh was since hunted down by Neo lords inside the complex, but was able to escape though it meant abandoning the exofighter. He makes his way to the geothermal processing plant and is able to destroy it, thereby destroying all the developing Neo lords as well. He is rescued by Stavrogan and DeLeon, while a bitter Praetorius is left to ponder future plans.

A combined e-frame/jumptroop mission to Antarctica to destroy the Neo warrior breeding complex becomes a disaster, as apparently only Yuri Stavrogan survives. Professor Algernon has made modifications to Alec DeLeon's e-frame, which provides a closer link between pilot and e-frame. Able Squad gets sent to Antarctica to try to locate the breeding complex. While planting a sensor which was to be part of a network, Marsh gets captured by some Neo warriors. Galba tells him to pretend to be Takagi, since all Neo sapien commanders have orders to hand Marsh over to Phaeton. To test the capabilities of a Neo lord, Praetorius has one duel with Marsh, who he believes to be Takagi. Marsh tries to escape, and his e-frame somehow contacts Alec's, and so Able Squad is about to attempt to get him. But Marsh gets defeated by a Neo lord, who forcibly removes him from his e-frame.

A mission for Marsh and Marsala to deliver an e-frame repair specialist to the resistance in Maine results in Marsh crashing in New York City and Marsala's capture by Galba. Livia sends some of the third generation Neo warriors to capture Marsh for Phaeton. Marsh runs into an old cabbie named Sidney, who helps him around. Marsh is able to dispose of the feline Neo warriors while on foot, but is given bigger problems by a winged one named Kor. Kor captures Sidney, but Marsh saves him and outflys the eagle warrior to defeat him. Galba injects Marsala with something that causes him to lose consciousness, and Galba tells Livia he is dead.

Both Marsh and Typhonus make seizing the alien technology their top priority. Both the exosquads and Neo frames make it to a central complex, and a battle follows. A fusion pack explosion in the core causes the alien complex to begin to self-destruct. Everyone tries to frantically escape, as the planet itself suffers from quakes and lava flows. Soon after the ExoTroopers and Torres with the ExoScouts escape, the planet Mars is destroyed in a gigantic explosion.

Able Squad blasts its way into the alien complex, and is pursued inside by Typhonus and his troops. After a battle which is made more difficult by interior defenses, Able Squad escapes into a different section. Meanwhile the alien structure begins to grow out of the ground. After the exosquad has blasted its way out and come to the aid of the jumptroops with Professor Algernon, the spire begins emitting great energy waves.

An attempt by the ExoFleet to covertly land e-frames on Mars to investigate a gigantic complex fails miserably, with most of the e-frames destroyed and pilots killed, because a spy tipped off the Neos to their arrival. That spy is Barca, who has Able Squad (the only survivors) captured, and proceeds to plot with Typhonus. The plan is to load a Neo ship, which Barca will claim to have captured, with explosives and then get it close enough to the Resolute II that it will be caught in the explosion. Hallas helps Able Squad escape, and the Neo ship destroys Barca's own ship rather than the Resolute II.

Napier escapes with Marsala. Despite his own objections, General Shiva complies with Phaeton's demand that he capture Marsh alive. Shiva offers to let everyone else within Parliament House go in exchange for Marsh, but Tyree refuses. The attack is launched and the resistance quickly loses ground. But Butler's company of jumptroops arrives, and they are able to capture Shiva. In exchange for his life, Shiva lets the surviving members of the Australian resistance go.

Torres, Bronski, and Takagi return to Canberra to provide air cover for a withdrawal attempt by the resistance. The attempt fails miserably, and they are forced to retreat back into the Parliament House. Weston stayed with DeLeon to try to fix his e-frame, and they come under attack by lizard Neo warriors. They escape to an aborigine camp, but are followed there. They lead the Neo warriors into a trap and destroy them with a rigged fusion pak. Napier escapes with Marsala in the cloaked e-frame.

The ExoFleet has taken Venus, but the Neo sapien Fleet, with Phaeton in command, prepares to counterattack. Barca sabotages the Resolute II, putting them in a precarious position. With Marsala pretending to be a Neo soldier who carries information about Draconis' plot against Phaeton, Able Squad boards the Olympus Mons II and cripples it. Algernon has since patched together the Resolute II, which proceeds to finish off the Olympus Mons II. Draconis escpaes, leaving behind Phaeton to be killed. When he returns to Earth with plans of ruling himself, he is met by the real Phaeton (the other was just a clone), who has him taken away, likely to be executed.

Sullust, Neo mega advisor to Draconis, sets a trap on Venus for the ExoFleet using the old GRAF station and a new one constructed by Enleal. Only aware of the one installation, Able Squad is sent to destroy the old station so that the approaching ExoFleet invasion force can launch its assault as planned. By the time they realize that the old station is a decoy, the new one as been activated. Unfortunately for the Neos it is useless against cloaked ships, and the ExoFleet is able to land its Jumptroops.

DeLeon and Weston are to take the captured Neo mega, Lysander, and a mutating agent back to the planet Chaos for examination. But what they believe to be Lysander is actually a melding of the Neo mega with a Neo sapien receiving experimental treatment for AutoMutation Syndrome. So during the flight back Lysander escapes and wreaks havoc on the Scavenger, killing various pirates, Captain Ryack included. The survivors abandon ship, leaving behind a overloading fusion pack to destroy the ship with the now mutated Neo aboard to be killed.

Able Squad arrives on Venus with the mission of locating and estimating every Neo base and troop concentration on the planet, as a prelude to invasion. While investigating a secret research facility Torres and Bronski are discovered, and in the battle to retrieve them Marsala is captured. He is taken inside, and sees that the facility is for research related to AutoMutation Syndrome (apparently a Neo sapien version of cancer). To prevent Marsala from divulging ExoFleet plans for an invasion Marsh sets out to destroy the facility with Marsala inside. Nara is unwilling to let Marsala be killed, and she goes to rescue him. She manages to succeed before Marsh finishes demolishing the complex, and on their way out she and Marsala unwittingly capture an experimental subject that merged with the Neo mega Lysander.

A replacement pilot, Yuri Stavrogan, preys on Kaz's hotshot tendencies, which results in his disobeying some of J.T.'s orders and causing tension between all three. The ExoFleet begins an assault on Mercury, and Yuri and Kaz make a point of trying to defeat Thrax, who is considered the best Neo pilot. The ExoFleet takes a Neo base on Mercury, but the Neo Commander Glycon launches a counterattack to draw in the ExoFleet e-frames so that Thrax and the Neo frames can attack the ExoFleet ships. The counterattack is foiled on the ground, but the Neo e-frames are able to attack the ExoFleet task force. Kaz, grounded by Marsh for disobeying orders, goes out to fight. He eventually finds himself in a dogfight with Thrax, and he loses when he gets blinded by the sun. Thinking that there has been enough destruction, Thrax chooses to spare his life.

Barca convinces Hallas to assassinate Simbacca, but only a serious wounding results. As Able Squad searches for Hallas, Barca attempts to lay a trap for them, but it results in the discovery that the Pirates have been building a gigantic Exo-Carrier (christened the Resolute II). Marsh convinces a recovered Simbacca to spare the life of Hallas.

After discovering that the resistance cell on Venus that they were supposed to deliver weapons to has been destroyed, Burns and Bronski are themselves captured. After a march with other captured Terrans, they arrive at a construction site, where Draconis is building a fortress he intends to use against Phaeton. The rest of Able Squad arrives to free Burns, Bronski, and the slave laborers, many of whom were in the resistance. The Venus resistance takes the large weapons stockpile and escapes.

A Jumptroop assault on Ceres results in the discovery of a new type of Neo, the Neo mega. It is captured and causes problems on the ship, until it is launched out a docking bay into outer space.

Marsh and Marsala coordinate with the Chicago resistance to free the imprisoned members of the Homeworlds Congress. Napier encounters Amanda Conner, his ex-wife, who is conducting interviews there.

Torres is put in the brig for attacking Jubail, who agrees to drop the charges as repayment of his debt to Marsh (who spared his life in The Embassy). Barca learns that the GRAF shield is inoperative, and is discovered by Jubail as he tells Typhonus. In the struggle that ensues Barca kills Jubail, and tells the guards that arrive that Jubail was the spy. Typhonus orders an attack on unprotected Io, and the ExoFleet abandons the base. When Typhonus pursues them, a Pirate fleet from Chaos decloaks on the Neos' flank, and starts to do damage tto he Neo fleet. The Neo fleet returns to Mars, where Typhonus is executed for his incompetence.

As the Pirate fleet leaves for Io, Simbacca tells Marsh to teach some pirates to fly e-frames. J.T. objects, citing the fact that e-frames are too complicated to learn quickly. Despite this, the e-frames are sent to prevent some Neo scouts from reporting back to Sinope, which is the site of a Neo Fusion Pulse Cannon. When the Pirate fleet is within range of the cannon, it begins to pick off Pirate ships. Marsh, DeLeon, and Hallas succeed in destroying the cannon, saving the fleet, as well as Io.

Typhonus offers a treaty of friendship to the Pirates in exchange for Marsh and DeLeon. When Simbacca refuses Typhonus' forces attack, wounding and capturing Simbacca. The Pirates plan to capture Marsh and DeLeon to trade them for Simbacca. Instead the two capture Hallas and use him to fool Typhonus into thinking that the Pirates succeeded and now wish to make the prisoner exchange. Upon docking the three fight their way to Simbacca's cell and free him. They try to fight their way out, but get stalemated by Neo troops. Alec uses his e-frame to send a message from Simbacca to the Pirates telling them to attack. The attack, led by Jubail, is enough of a diversion to allow them to escape. Once they arrive back on Tethys Simbacca announces that the Pirates will enter the war on the side of the ExoFleet.

Marsh and DeLeon leave Io to contact Simbacca and secure an alliance with the Pirate Clans. The rest of Able Squad is picking up resistance leaders from different locations on the Homeworlds, taking them to Io for a meeting with Admiral Winfield. Typhonus, who was ordered by Phaeton to find where the ExoFleet was hiding, follows them to Io and then begins to attack the ExoFleet base. Winfield orders the activation of the GRAF shield, which forces Typhonus to order a retreat. Marsh and DeLeon get picked up by the pirates, and Barca reports this to Phaeton.