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.

The Exofleet pursue the pirates back to their base. Napier prevents an assassination attempt on governor Phaeton.

Marsala takes control of the space tug and saves the container, crash landing on Venus instead. Nara goes off on her own to locate her family, while the others try to locate her thinking she was shot down.

Marsh, Burns, and Marsala go to South America to retrieve a Terran geneticist named Ketzer, who the ExoFleet hopes will help them discover a weakness in the Neo lords. Although they destroy a Neo patrol they encounter, Draconis becomes aware of their presence in the rain forest. The three are then attacked by green humanoids, who succeed in capturing Nara. They take her to their village. She awakens with her arm hurting. Ketzer is there, for it was he who altered the natives, as well as himself. Ketzer notifies her comrades of her whereabouts, and they soon arrive. The Neos also pick up the signal, and Draconis is convinced by Medusa that he will be rewarded if he were to personally lead a successful attack. Medusa then reports to Livia that Draconis only serves for the sake of his own gain, not out of loyalty. Ketzer asks for the help of the ExoTroopers in attacking the nearby city Manaus. When they refuse he reveals that he has injected Nara with a retrovirus that will alter her DNA to make her like them, but has a compound that will prevent it if they help him. Just then the Neos launch an attack on the village, forcing both the villagers and the exotroopers to flee. Draconis is killed for disloyalty on Livia's order by a group Neo lords, ending Neo pursuit. Marsh tells Ketzer to recreate the compound that will cure Nara, but Ketzer says that he lied when he said there was a cure. Marsh wants to take Ketzer back to the ExoFleet, as were his orders, but Ketzer escapes when his altered humans distract the exotroopers with the possibility of an attack.

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.

A series of raids on commerce vessels prompts the Earth Homeworlds' General Assembly to send the entire Exofleet to wipe out the pirates once and for all.

Able Squad is stranded on Earth after distracting the Neo fleet, to allow the Exo-carriers to retreat. They make contact Napier's resistance, but get a cold greeting, as the Earthers blame them for leaving the planet unprotected.

After 1 year in the brig for insubordination, Able Squad is back in action. Marsh, Marsala and Deleon get the first mission - to return to Earth and disable the newly built planetary defense shield with the help of the Earth resistance. But when they're ambushed at the rendezvous point, people start suspecting there's a traitor in their midst.

After hijacking a transmitter to warn Exofleet about the Venus Grav Shield, JT, Alec and Marsala try to get off Earth by sneaking aboard a prison transport. The rest of Able Squad is sent to Venus to locate the shield projector installations.

The General Assembly commissions Exosquad to eliminate the Tethysian Pirate.

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.

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 imminent, 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 follow-up 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.

Getting hammered by the pirate base's defenses, the Exofleet sends down Able Squad to take them out. The Martian finance minister discovers someone has been taking massive funds from the Neo-Sapian treasury.

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

Napier and the Resistance commence the battle to liberate Earth.

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.

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.

Nara is reunited with her brother, James as Able Company attempts to deactivate the Graf Sheild surrounding Venus.

Captain Marcus is angered by Admiral Winfield's decision to not attempt to liberate Earth, which he perceives as cowardice. After sending Able Squad (minus Weston and Takagi) on a secret mission to Mars as a way of getting rid of Marsh and other Winfield supporters, Marcus mutinies with the support of at least one other captain and most of the Resolute's security forces. The mutiny succeeds, with Winfield and his supporters (including Weston and Takagi) being locked in the brig. Able Squad reaches Mars, and the episode ends with them fleeing pursuing Neo e-frames.

Marsala and Phaeton square off; Marsala proves his allegiance.

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.

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.

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.

The Exofleet races back from to Earth from Saturn, hoping to return in time to stop the Neo-Sapien attack. Marsh gets charged with mutiny when he disagrees with Captain Marcus' decision to split the fleet, sending the fastest ships ahead of the rest. Napier escapes from a work camp and tries to organize a small resistance cell.

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.