The General Assembly commissions Exosquad to eliminate the Tethysian Pirate.

A pirate spy for the Neosapiens threatens Marsh and DeLeon's mission. The Exofleet is blockaded on 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.

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.

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.

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.

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.

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.

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.

Torres arrives in Phaeton City to coordinate with the resistance there, with the objective being the capture of a Neo mega. Anticipating this, Shiva's Neo mega advisor, Lucullus, sets different traps for them. One of these allows the Resistance to capture Sulla, who can then transmit the location of Resistance headquarters. Upon receiving its location Shiva launches an attack which Lucullus believes to be premature. When Napier returns from a meeting with other Resistance leaders he is able to take advantage of his unnoticed approach from behind the Neos to help his own troops escape the Neo attack. For his failure to capture the members of the Resistance, Shiva is replaced by Livia as Commanding General of Earth Forces.

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.

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.

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.

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.

The ExoFleet is having success in its campaign on Venus. James Burns leads the Venus resistance in an attack on Vesta, and he is severly wounded by Draconus in the process. Knowing that the ExoFleet will take the city, Draconus orders Thrax to detonate a hydrogen bomb, but after much thought Thrax does not obliterate the city. Phaeton arrives with the Olympus Mons II to prepare a counterattack.

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 escapes, 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.

Phaeton's scientists have succeeded in creating a Neo sapien that looks like Alice Noretti, who was a member Able Squad when she was killed. Phaeton places her on a Terran worker transport, having learned that the Resistance plans to free the workers. Phaeton assumed (correctly) that she would be placed back with Marsh's squad, and since Marsh was a favorite of Winfield it would only be a matter of time before Noretti got the opportunity to assassinate Winfield. Meanwhile the Marsh/O'Reilly romance seems to progress, but is hindered by the arrival of Noretti. Marsala begins to notice clues that indicate Noretti is a Neo, but Marsh is in denial when Marsala shares his suspicions. Winfield decides to go to the Venusian surface to examine the situation and mingle with the troops, and of course expects to meet Marsh. Noretti acts, and has the opportunity to kill Winfield. But an identity crisis prevents her from doing so, for she embraces her Alice Noretti persona. She then tries to fight her way past various e-frames and jumptroops, but after getting hit by O'Reilly her e-frame crashes into the canyon wall, killing her.

Marsala is kidnapped by former members of the Venus resistance, who demand that all Neo sapiens, whether loyal to ExoFleet or not, be deported from the planet. James Burns, who has been fitted with prosthetics, decides to help his sister and try to rescue Marsala alone. He is able to infiltrate the kidnappers' ranks by pretending to be sympathetic to their cause, and later tries to sneak Marsala out. Some Neo sapien holdouts attack the encampment, and though James is able to save Marsala, it is at the cost of his own life.

Nick Tyree, leader of the Australian resistance, disobeys orders from Napier and the ExoFleet and proceeds with an uprising throughout Australia. Able Squad and Napier go to Australia to try to convince him to pull back before the Neo sapien counterattack. Whether Tyree would have or not is moot, since Phaeton's response arrives in short order. He unleashes new warriors, genetic mixes of Neo sapiens and different predator species. The resistance forces that are able withdraw to Canberra to make a stand there.

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.

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.

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.

The capture of Marduk, a Neo sapien who has supplied the ExoFleet with information, prompts Winfield to send two exosquads to Mars. Eventually Typhonus uses the spy as bait to ensnare the exosquads in a trap, but is not entirely successful. Torres gets shot down and rescued by some ExoScouts.

Torres, believed dead by her fellow ExoTroopers, takes charge of the ExoScouts that found her. A few of them resent this, and while she tries to lead them all to her exosquad, they arrange for her to have an accident that they believe results in her death. The ExoScouts are then captured by a group of raptor Neo warriors, which had been dispatched by Typhonus in the hopes that the ExoScouts could reveal the location of the exosquads on Mars. But Torres is not dead, and she manages, one by one, to free the ExoScouts who then truly follow her. Meanwhile, Able Squad and the remainder of Baker Squad have arrived at the site of what they believe to be an underground Neo complex, but they discover that it is something far more unusual.

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.