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.

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.

Able Squad continues to flee from Neo sapien e-frames on Mars, and eventually they find shelter in a cave. Captain Marcus orders the ExoFleet to set a course for Earth, so that they can liberate it. Phaeton knows that the ExoFleet cannot withstand the Neos combined strength, and so he orders the Mars Fleet to Earth to assist (which results in the Neo frames halting their pusuit of Able Squad). The fleets engage near Earth, and the Neo sapiens are clearly victorious, inflicting devastating losses on the ExoFleet, whose few remaining ships attempt a withdrawal. The only Neo losses occurs when Marcus destroys the Resolute in the vicinity of many Neo capital ships, which are also destroyed. While covertly searching the Neo sapien complex, Alec and Marsala find thousands of brood chambers. The episode ends with Marsala sounding an alarm which brings Neo guards (who capture the two), demanding to see Phaeton, and declaring that he will save his people.

The remnants of the ExoFleet escape and, once he has put down the mutiny, Admiral Winfield has the fleet set course for a return to Io. Marsala is taken to Phaeton, who is hesitant to believe that Marsala has changed sides. Marsala captures the rest of Able Squad, and Phaeton has Marsala conduct a brain scan of Marsh to determine if his defection is deception. When Marsala is given the opportunity to execute his fellow squad members he makes an impassioned speech regarding the plight of the Neo sapiens, but then turns against Phaeton. The rest of Able Squad rushes the guards and they take control of their location. At the end, Typhonus is sending troops to the area, giving orders to shoot to kill.

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.