The war is over and thus begins the task of rebuilding.

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.

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.

Marsh is being held prisoner; ExoSquad begins its final assault.

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.

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.

The General Assembly commissions Exosquad to eliminate the Tethysian Pirate.

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 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.

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.

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.

J.T. Marsh and the ExoSquad attempt to destroy Phaeton's Doomsday device.

Captain Butler and the jumptroops try to take over Washington, D.C.

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.

Marsh finds himself in New York, facing down a group of Neo-Warriors sent to hunt him down (you'd think he threw Phaeton off a mountain or something). He encounters the last cabbie in New York, Sidney. Marsh eventually outwits the Neo-Warriors but the Torch on the Statue of Liberty is destroyed in the process. Marsh makes his way to the Resistance, while Sidney stays in New York.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.