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.

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

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.

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.

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.

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.

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.

Marcus is able to lead the fleet straight into the heart of Neosapien flagship territory.

Marsala and Phaeton square off; Marsala proves his allegiance.

Able Squad escapes from the brood chamber with Phaeton as a hostage (a useless one, since Typhonus wouldn't mind him dead). Once outside Phaeton tries to resist and is shot, he then falls down the mountainside. Able Squad climbs up the mountain so they can destroy the brood chamber. They then realize they can accomplish this by flooding it with magma. Phaeton returns to try to stop them, but J.T. defeats him in an e-frame battle. The mountain then explodes, and Weston and Takagi arrive just in time to pick up their fellow squad members. The episode ends with a preview for next season with Marsh and Typhonus each receiving missions from their leaders.

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.