Rita Torres is flying through an asteroid field in an e-frame slightly different from her usual frame, and she is being pursued and fired on by Pirates. She turns and shoots, destroying one Pirate. As she turns to target another, an older e-frame pilot named Valentine comes to her assistance by destroying another Pirate that was approaching Torres from behind. He is soon hit, however, and his e-frame loses its arm and he quickly goes down. Torres realizes he is dead, and angrily attacks a group of Pirate ships. In short order she is hit in the back and her e-frame crashes on one of the larger asteroids, and the damage is so bad it takes all her effort to turn the e-frame over. A Pirate ship lands nearby, and its pilot approaches her. It is Jubail, and he tells her that while he could just kill her, he would much prefer to think of her dying slowly by running out of air. With that he strikes her e-frame's windshield with the butt end of his blaster, cracking the windshield and allowing air to slowly escape. Torres wakes up with a start, and walks over to a framed picture sitting nearby. It was her first squad, and Torres states that she will never forgive Jubail.
A Neo fleet is still in place around Io. Inside the mess hall, a group of Pirates surround Jubail's table and laugh loudly as he tells them a story about a battle in which he was involved. At a table not too far away sit Torres, Bronski, Weston, and Takagi. Wolf Bronski complains that the Pirates act like they own the place despite being there for only a day, and Kaz Takagi stands and says, "Maybe we oughta go show 'em whose base this is." Torres tells Kaz to sit, and he loses his angry tone and pleads, "Aw Sarge, somebody needs to teach those guys some manners." Torres says angrily, "There's only one way to teach a Pirate anything -- over the barrel of a blaster!" but then reminds them all that the Pirates are their allies now. Jubail's story continues with, "And then he tried to surrender!" and the pirates around him laugh some more as a look of rage is seen on Torres' face.
In Able Squad's landing bay, Torres and Weston are working on their e-frames. They have a quick chat as J.T. Marsh walks in with a group of Pirates, with Jubail in the lead. Marsh tells Torres that Winfield told him to give the pirates a tour and he thought they might like an e-frame demonstration. Torres argues that they can't do that because once the war is over the Pirates will use the ExoFleet's own secrets against them. Marsh puts Torres back in her place with a simple, "Sergeant!" and Torres climbs into her frame and Jubail jokes that he would like to see a working e-frame since when he sees them they aren't operational for long.
At this last joke Rita punches Jubail, and he is sent flying across the room. She approaches him and prepares to crush him by stepping on him, but Marsh catches up with her from behind and pulls the fusion pack out of her e-frame robbing it of its power. The e-frame falls and Torres climbs out. Jubail says he wants her arrested, and a pair of pirates grab hold of her as she protests.
Later, Marsh comes to visit her in the brig. She tells him that she was on her first e-frame mission when a small mistake by the squad's commander led them into a Pirate ambush and she was the only one to survive. She tells Marsh that Jubail was the one who led the ambush. Marsh says that even if she faces a court martial he will do what he can to help her since he and the squad need her. He laughs and says, "At least you didn't hurt him." Torres responds, "It wasn't because I didn't try."
Marsh goes to Winfield and asks him to let Torres go, and he promises she won't do anything like it again. Winfield says that Marsh can't make that guarantee, but J.T. tells him that Rita's problem is only with Jubail and that she can learn to work with other pirates. Winfield says he can't let her go because it would jeopardize the alliance and they need the Pirates help. Marsh asks what he would do if he could convince Jubail to request her release. Winfield smiles and knows J.T. is up to something and says, "Then I'd have to go along with it, for the sake of the alliance."
Aboard Typhonus' flagship he is eating with his officers when he has a revelation. He states that a target that cannot be attacked from the outside must be attacked from within. He contacts Barca, the pirate spy for Phaeton, who complains that he only takes orders from Phaeton. Typhonus says that he commands that sector, and so Barca is obliged to follow his orders as well. Barca says that bringing an end to the alliance is as simple as killing Simbacca since Jubail has no love for the ExoFleet. Typhonus is not interested in this, however, and tells him to disable the GRAF shield protecting Io and that the Neo fleet will do the rest.
Meanwhile Jubail speaks to Simbacca, inciting a group of Pirates who watch the two of them. Jubail says that the attack on his life proves that the Pirates and ExoFleet cannot coexist, and that they should all leave Io and return to Tethys. Just then Marsh walks in, and Jubail wants him to leave since he is not a Pirate. Simbacca states that he has earned the right to speak, and Marsh pushes his way past the guards. He says that according to the Pirates' own code of conduct, Jubail owes Marsh a debt for having spared his life, and so Marsh is asking Jubail to drop the charges against Torres and to never seek revenge against her. Jubail at first refuses, but when Marsh begins to walk away saying his debt remains unpaid, Jubail relents. Jubail leaves the room angrily, and Simbacca tells Marsh that while Jubail will keep his word he is still Marsh's enemy and so Marsh would have been better off having killed Jubail when he had the chance.
Algernon is still busy trying to repair the GRAF shield, and isn't pleased by the distraction Maggie Weston causes as she tries to work her way past the guard at the door to lend Algernon a hand. Algernon says he doesn't need an assistant, but rather the proper equipment. He tosses Weston the component he has just removed and asks her what she makes of it. She coolly states, "I'd say an N-wave parametric regulator with fused cryosynaptic relays." "Exactly. And the whole system's like that, junk! I told the Admiral this might happen without the proper tests, but did he listen? No. But I'm only the scientific genius who built the GRAF shield, what do I know?" "Weren't we under attack at the time?" Maggie asks to explain Winfield's decisions. Sounding no less annoying Algernon says, "A technicality. The intrusions of the outside world have no place in science." Quite annoyed herself by now Weston asks, "All right, so what do we do to fix it?" "Fix it? The GRAF shield cannot be repaired. I should know, I've been trying to repair it." Weston just says, "Well, let's just hope the Neos never find out." But in the shadows on a catwalk above is Barca, and he leaves having heard what he wanted to hear.
In the conference room Winfield sits at one end of the table with Simbacca at the other. Sean Napier, Nick Tyree, and James Burns sit on one side of the conference table with Jubail and another pirate at the other side. Simbacca states, "We want Mars. It's the least you can give us in return for the support you need from us now." Winfield asks, "What about the Neo sapiens who live there?" "Exterminate them. Isn't that what one usually does to a defeated enemy?" Winfield stands and approaches Simbacca's end of the table, saying, "We're not fighting to slaughter Neo sapiens, we're fighting to end Phaeton's tyranny." Simbacca asks with a smile, "What will the Neo sapiens do to you if they win? To the victor belongs the spoils." As Napier stands and walks next to Winfield he says, "The Pirates can share Mars with the Neo sapiens. After the war there'll be plenty of room for both of you. I've fought the Neos face-to-face, whatever else you may think of them they've got guts. Besides, there won't be many of them left."
Simbacca considers for a moment before saying, "All right, agreed. We get Mars in exchange for the outer worlds. All except one, that is. There is one world that the Neo sapiens must never rule." Jubail stands at the table and shouts, "Simbacca, no! You're betraying our secrets to outsiders?" Simbacca tells him, "If we're to be allies, Jubail, they must know everything." "Fool! When the Neo sapiens have been eliminated who do you think the ExoFleet will fight next!" shouts Jubail before he storms out of the room. Intrigued, Winfield asks, "Simbacca, what world could cause such concern?" Simbacca tells him, "Your homeworld scientists have searched for a tenth planet beyond the orbit of Pluto. We Pirates found it, and we call it... Chaos. It's composed of dark matter which makes it almost invisible. Dark matter gives our Pirate ships the ability to cloak. We offer it to you as a safe haven for your fleet to refit and rearm." Winfield says, "I accept it," and the two shake hands to cheers. Winfield says, "Now, at last, we are united."
As Jubail walks down a corridor he sees Barca run down an intersecting hall into a storage area. Curious, he follows him. Thinking himself hidden among some crates Barca activates his holographic transmitter and contacts Typhonus. He tells him, "The time has come, Typhonus. The GRAF shield on Io is inoperative, at last you can..." but is interrupted when Jubail shoots the transmitter. Jubail says,"I was looking for you, Barca, to warn you Simbacca has betrayed the secret of the dark planet to the ExoFleet. Don't you find that ironic, traitor?!" Barca tries to explain his actions, stating that for the Pirate Clans to survive they must be on the winning side and it is the Neo sapiens who will win. Jubail says that Barca makes him sick, for at least Simbacca doesn't hide what he's doing. Jubail then walks to a nearby panel and triggers an alarm, but Barca has a pistol spring forth from his forearm armor directly into his hand and fires, knocking the blaster out of Jubail's hand. Jubail then jumps at Barca, and a struggle ensues. A shot is fired, and it is Barca who is left standing. A security detail then arrives, and Barca fingers Jubail as a spy who he found contacting the Neos.
Meanwhile Typhonus, with knowledge that the GRAF shield is inoperative, orders an all-out attack on the ExoFleet.
In the conference room Winfield is telling those gathered there that to defeat Phaeton they must organize a systematic campaign that best utilizes each arm of their allied force. He is interrupted, however, by a message stating that Jubail was slain while contacting the Neos. Simbacca says he never would've believed such a thing, but Winfield is more concerned by the status of the Neo fleet. When a check reveals they are getting underway, Winfield orders an immediate evacuation. Winfield then tells Marsh that the e-frames must buy time for the evacuation, and so J.T. salutes and runs off.
Able Squad arrives at their hangar, and they each frame up. Bronski comments, "Man, it's just another day at the office. Savin' everybodys' butt." Hallas states that the coming battle will decide the fate of the solar system. They gather and Marsh tells them that they're cover for the whole fleet so there's no turning back. They fly off and engage the Neos. With a group of shots Bronski manages to destroy a cruiser. Soon more Neo e-frames are launched, and Marsh tells his squad to keep them away from the shuttles, but at least one is destroyed before Able Squad can engage. Torres soon finds two Neos on her tail, but Hallas manages to destroy both and Torres finds herself thanking a Pirate.
With Io evacuated Admiral Winfield orders the ExoFleet to disengage and scatter. But then Simbacca appears on Winfield's communications screen and tells him that the fleet must follow his course. Winfield reasons that if they scatter some will escape to make it to Chaos, but Simbacca just tells him to trust him. Winfield cancels his previous order and tells the fleet to follow the Pirate flagship. They proceed to do so as Typhonus watches them and orders his fleet to pursue as he vows that they will not escape.
With the Neo fleet gaining, Winfield contacts Simbacca and tells him to continue the fight should the ExoFleet be destroyed. "You talk of failure too quickly, Admiral." says Simbacca with a smile. Winfield attributes it to his being a realist, and says that he will transfer the e-frames to the Pirate ships, who can then cloak and escape. He says the ExoFleet will engage the Neos so the Pirates can make good their escape. Simbacca says, "You are a brave man, Admiral, to sacrifice yourself for our escape. But it will not be necessary." Just then a group of Pirate ships surrounding the Neo fleet decloak and attack. Marsh is pleased and congratulates Simbacca.
A group of Pirate destroyers destroy a Neo carrier, and even Typhonus' flagship takes a number of hits. Typhonus wonders where they came from, but soon orders his ships to withdraw. As they do so a few more cruisers are destroyed by the Pirates. Typhonus swears, "There will be another day. This is not over."
Winfield jokes with Simbacca regarding him not being completely honest back on Io, and Simbacca admits that there were things he didn't feel Winfield needed to know and that the ships coming from Chaos were his secret. Winfield then compliments Simbacca's deviousness.
Back on Mars, inside Phaeton's palace, Phaeton is angry with Typhonus' bungling since he has brought the Pirates into the war on the ExoFleet's side and has failed to deliver Winfield. Typhonus is held be two guards, but he manages to trip one and knock out the other. He starts, "The Terrans are more clever than we thought, Phaeton. Next time I will..." "For you, fool, there will be no next time." Phaeton then activates a device with a remote he holds in his hand. As a device lowers from the ceiling Typhonus pleads, "I'm your best General, you need me." "You're right Typhonus, I do need you. But which you?" says Phaeton as he reveals a number of breeding tubes, each with a (fully clothed) Typhonus inside. The device over Typhonus' head powers up as he cries, "But Phaeton, I... AHH NOOOO!" as he is vaporized. Phaeton turns away and says, "Goodbye, Typhonus. And hello..." as he releases one Typhonus from his tube.
The final scene is of the allied fleet arriving at Chaos, and Simbacca welcomes Winfield to their new home.