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.

As a prelude to the assault on Earth, the Exofleet retakes the moon.

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.

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.

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.

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

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

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.

Phaeton gives orders to Lucullus to begin work on a bunker underneath Phaeton City. Marsh attempts to rendezvous with Marsala and Felson in Maine, but realizes Turner's treachery and is able to escape the trap set by the Neos. The Neo megas claim Marsala's body, and take him to their base on Maniton Island, where they revive him. Galba and the others explain that they want him to kidnap Phaeton, for he will not surrender despite the fact that the Neo sapiens are losing the war. That way they can take charge and make peace. Marsala reluctantly agrees to their plan. Meanwhile Picasso has discovered that Phaeton is in the tunnels beneath the city. Once he notifies the Resistance they mount an operation, including Marsh, to go after Phaeton. Beneath Phaeton City, the Resistance attacks and Phaeton blames Lucullus and Gracchus. As Phaeton goes to join the battle he is ambushed by Marsala. Lucullus and Gracchus use the confusion to try and shift the blame for the Resistance assault on Livia. Phaeton is able to escape from Marsala by exiting his e-frame and utilizing the fact that the Auto Mutation Syndrome has somewhat liquefied his body to enter a sewer pipe only a few inches in diameter. As Marsala is leaving he comes across the Resistance in full retreat, and their chances of escape do not appear to be good. Marsala fires a few missiles to collapse the tunnel on the pursuing Neos. Lucullus and Gracchus, assuming that Phaeton is dead, begin to organize a purge. Phaeton arrives on the scene, however, and has them arrested instead.

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.

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.

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.

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

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.

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 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.

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.

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 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.

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.

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.

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.

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

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.