In Canada, at Great Slave Lake, Kaz Takagi is building a funeral pyre for his fallen friend Yuri Stavrogan. When he hears a sound behind him he pulls out his blaster as he turns, but it is only Marsala. He reports that Yuri is dead and J.T. Marsh has been captured and was taken east. Marsala knows that Marsh will be taken to Phaeton, and Takagi climbs into the rear seat of Marsala's e-frame. As they take off the pyre alights with flame, and Takagi shuts his eyes as tears well up. As they fly off in the background we see pictures of their lost comrades (Marsh, James Burns, DeLeon, and Stavrogan).
At Phaeton City (formerly Chicago), in Phaeton's bunker, Marsh awakens. Phaeton is standing nearby, and he greets him. Marsh is on a circular platform with bars of green energy forming his cell. Phaeton says, "An inferno rages inside me, Terran. It consumes me, burns me." Marsh just replies, "Probably something you ate." Phaeton tells him, "I will destroy you with my own hand, and then I will destroy your world," and the look on his face is the grin of a madman.
Marsala and Takagi fly toward the Resolute II, passing nearby the many energy blasts that pound the Earth's surface. Once aboard they go to a hangar where Admiral Winfield is briefing a few e-frame squads. He informs them that despite heavy losses, the attack is on schedule. He says that while rumors of Neo lords turning against some senior officers in a sort of purge may be true, and there are groups of Neos surrendering, there is still work to be done. When Takagi reaches the line he stands next to Maggie Weston, who says, "I'm glad you're alright." Kaz responds, "Me too," at which point Winfield clears his throat loudly, and all the other pilots in the room being laughing loudly, including Nara Burns and Rita Torres. After it dies down, Winfield continues. He says that their success is meaningless if Phaeton has a doomsday device. He says that they failed to locate this device, so the opposite approach must be taken. While resistance groups are converging on Phaeton City, they don't have enough firepower to take his bunker. So, Winfield says, "Ladies and gentlemen, you're going after Phaeton!" and the group begins cheering, with Marsala standing rigid as ever.
In Gettysburg, Pennsylvania, Wolf Bronski exits the jumptroop shuttle, angry. He finally contacted Lieutenant Burns and found out from her that they were going after Phaeton. Colleen O'Reilly asks about J.T., and Bronski tells her he was captured. She tells him that she's fixed the shuttle well enough that it can get them there. She walks over to Longfeather, and asks him how their commander, Avery Butler, is doing. Captain Butler sleeps fitfully and is sweating, and Longfeather figures he has a fever and comments on how the Neo lords probably don't keep their claws clean. O'Reilly tells him that she is taking the remainder of the squad to Phaeton City and that he should care for the wounded there.
The column of resistance e-frames and tanks coming from Detroit is one of those groups converging on Phaeton City. Sean Napier tells Eve Hanley that the ExoFleet has requested someone from the Chicago resistance, someone familiar with the sewers and tunnels under the city. She offers to go, and he wishes her luck.
Inside Phaeton's bunker, Livia tells Phaeton the armored column continues to advance and she begs him to leave the city before it is surrounded. As Praetorius enters she asks him to suggest to Phaeton that he attempt escape so that he can continue to lead the Neo sapiens in their struggle from elsewhere. Phaeton talks of how after the first Neo sapien war those who did not surrender were hunted down like animals. When she speaks of how he was the reason the recovered he snaps angrily, "Do not defy me Livia!" She seems on the verge of tears when she tells him she just wants to save him.
Just then the bunker rocks with hits from the Resolute II. Winfield then orders the weapons to cease firing, and leaves the task to his launching e-frames.
Back in the bunker Phaeton speaks to those who are his last line of defense, "Shiva, you have always been my best general. Can you stop them?" Shiva's reply is, "No, but I will try." Draconis accompanies him in this task. Livia puts her head in her hands in sadness.
Outside, Neo e-frames, rocket infantry, and Neo lords attempt to hold off the ExoFleet e-frames. Torres flips a Neo lord off her back. Hanley arrives, blasting a Neo frame as she does. She reports to Nara that she is there to guide them through the tunnels, and they proceed to follow her.
Back inside Phaeton says that all the ExoFleet will get back is a burned cinder, and he tells the computer to arm the detonator. A device with a pink glow surrounding it is lowered from the ceiling. It is Phaeton's doomsday device, antimatter contained within a magnetic field. Phaeton tells Marsh that when he flips the switch the magnetic field will be cut and the antimatter will be released, thereby annihilating the planet. Marsh shouts, "No! Phaeton!"
Phaeton flips the switch, but nothing happens. He is shocked and immediately knows it is sabotage. Livia says she will see to its repair, and just then he realizes it is she. He blasts her, saying, "Everyone betrays me in the end. They are all traitors... traitors." He orders Praetorius to repair the detonator, and he goes to work. Phaeton then tells Typhonus he has gathered some traitors at New Soldier Field, and they should be executed as they are not worthy to meet the end with him.
At New Soldier Field there are many wounded and disheveled Neos sitting under Neo lord guard. Galba is brought among them and thrown down. Thrax goes to him, as Galba wonders why they are being kept alive, and not simply executed immediately. "He keeps us alive to give us time to be afraid," is Thrax's explanation. Galba laments not having been executed with the rest of his brood brothers. Thrax tells him, "I used to worry how I would face the end. Would I go bravely like a soldier? But let me tell you something Neo mega, it's life itself that matters, not how it ends. Each moment is a precious gift, if only we have the courage to accept it. That is where our duty lies, not in taking life, but in living it."
Then Typhonus announces to all of them that they are to be executed for being traitors. But the resistance armored column bursts in, diverting attention. Thrax stands and yells to his fellow prisoners to go to the tunnels, and waves them in the proper direction. Some Neo lords are ready to kill the prisoners despite the immediate threat, but Napier barks orders to keep the Neo lords away from the prisoners and the resistance is successful. As the resistance and Neo lords exchange fire, the prisoners stream out of the stadium as Thrax and Galba wave them along.
As Hanley leads the exotroopers through the tunnels she says that if Phaeton used the old subway grid his bunker may be under the central station. Marsala notes that Phaeton lacks imagination and so likely used the old subway plans. The group then encounters some Neo sapien e-frames, Shiva and Draconis among them. Burns gives orders to keep moving, and Draconis notes there are too many exotroopers. Shiva gives instructions to hold their ground as long as possible, saying he will take an alternate tunnel to get behind the exotroopers and attack their rear.
Meanwhile Bronski and Charlie Company arrive in Chicago. As large explosions rip through the city, Wolf jokes, "Man, you can always tell where the squad is." They approach the aboveground entrance to Phaeton's bunker, over which the phrase Phaeton had engraved only partially remains. Vince Pelligrino reads what is there, and O'Reilly completes the quote. "Abandon all hope, ye who enter here. It's Dante, from the Divine Comedy" "Sounds like a load of laughs," remarks Bronski, and he blasts all but SPERANZA, which is the Italian word for hope.
They proceed into the tunnels, where Shiva and a few other Neo frames have succeeded in getting behind the ExoFleet. They attack from behind, catching them off guard and doing some damage, to Hanley and Weston in particular. But Bronski and Charlie Company then arrive to begin an assault on their rear, forcing the Neos to try to withdraw. This is prevented, and when Shiva's frame is disabled he says to Bronski, "Fire Terran, I... I have no wish... to live." Wolf just smiles and tells him, "Too bad."
In the front, Burns and Marsala (with Takagi still in the back seat) each take quite a few hits. Torres begins to advance, and despite taking numerous hits continues advancing and firing, destroying one e-frame as she does, until she reaches Draconis'frame and smashes in the cockpit, causing it to explode. The explosion knocks her into the tunnel wall, and her e-frame collapses to the ground.
Inside the bunker, Phaeton asks Livia why she sabotaged his doomsday device. She says that she still believes in the Neo sapien order, in their superiority, and in their destiny to rule. She says that despite this defeat they will rise again. Phaeton speaks coldly, "Let me tell you a secret, Livia. There is no Neo sapien order, no destiny. There is only power... my power. I did trust you, Livia, that's why I never made any clones of you." He then exits the room, and Livia goes to follow him out. But she is met by two Neo lords, and all she can do is react with shock.
Phaeton enters the main room and asks, "Have you ever known happiness, J.T. Marsh?" "Not since I met you," Marsh replies. "I was happy... once. It was after the first Neo sapien rebellion, I was invited to speak at the University of Chicago on the future of Neo sapiens. Before the speech I took a walk. It was a beautiful day and the sun was warm, I heard bells in the distance... and for a moment I was at peace.
The bunker suddenly shakes, presumably from a nearby explosion. Praetorius then informs Phaeton that he has repaired the detonator, and he approaches it. Marsh yells after Phaeton, "Phaeton! I thought you were going to destroy me with your own hands!" Phaeton observes, "You are trying to delay me. But how long does it take to crush an insect?" He then reaches into the cell with his e-frame arm, grabbing Marsh and ripping him through the energy bars as he shouts in pain. "Too bad you won't be here to see the most important event in the history of the solar system!"
Just then Burns and Marsala blast into the chamber, and Marsala says, "Surrender, Phaeton. You have lost." Phaeton shouts, "I will never surrender!" as he throws Marsh to the side. Two Neo lords and even Praetorius fire blasters at the intruding exotroopers, and after Burns dispatches one Neo lord, Phaeton also shoots at Burns, knocking her out of the room. Marsala rushes Phaeton, and their e-frames struggle with each other. Then a Neo lord blasts the right side of Marsala's frame, which then falls on its left side. The Neo lord jumps on top of the cockpit to finish off the pilots inside, but Marsala is able to hold his own for the short while until Takagi uses the e-frame's guns to knock some of the ceiling on top of the Neo lord. Praetorius flees falling fragments of ceiling, dropping his blaster as he does, but is unable to evade all of it and is at least trapped underneath (we are perhaps meant to interpret this as his death, since there is a view of the pile of rubble and his dropped blaster). Phaeton emerges from some of the rubble proclaiming, "You cannot defeat me. I can still destroy you all!"
Marsh has taken this opportunity to climb into his e-frame, and as he odes he shouts, "It's over Phaeton, you're finished." He then launches himself at full speed into Phaeton, slamming him into a control panel. Phaeton lands a few punches to Marsh's frame, damaging the shoulders, but Marsh then shoots him off. Phaeton gets up quicker, stands over Marsh and says, "Now I have my revenge, J.T. Marsh, first you, and then your Earth!" Marsh then uses his gattling gun to score multiple quick hits on Phaeton's frame, which spins and lands on the front of J.T.'s frame.
Phaeton the exits his own e-frame and slithers his way to the control panel, as the Auto-Mutation Syndrome has almost completely liquefied his body. He rants, "I will destroy you, I am Phaeton!" Burns reenters the room and Marsh shouts, "Nara, stop him!" As she reaches for what was Praetorius' blaster, she clutches her left arm in pain, and gasps Ketzer's name. Phaeton reaches for the control panel, saying, "With my last breath, I destroy you all!" Nara shouts, "Noooo!!!!" and her eyes begin glowing and she reaches out with her right hand, which also develops a green glow. Inches from the switch Phaeton's right hand is also surrounded by a green glow and it is frozen in place. She takes the blaster in her left hand and walks up to him. He looks at her and says, "You... you aren't human." She says, "My mother and my father were... and my brother." Just then her eyes and hand stop glowing, as does his. Phaeton is either still stunned or just surprised once more, but he makes a grab for his own hand blaster. Nara ducks his shot, and proceeds to fire two of her own, finishing him. "My brother's name was James," she ends. Nara exhales, and tosses the blaster to the side as she walks toward her comrades fallen e-frames.
Next we see Bronski and Hanley climb out of a manhole cover. He begins running, prompting her to ask where he's going. "It's all over," he says, "somebody needs to make some noise." He begins ringing some church bells, and she lends a hand. The scenes then progress to different parts of the world, from Sydney (not the city, the cabbie Marsh met in New York) honking his taxis horn, to Paris's Notre Dame Cathedral, to a temple in Japan, to the city of Sydney in Australia.
It is now morning in Chicago, and an ExoFleet shuttle lands. Winfield and a couple other high-ranking ExoFleet officers exit, while Marsh and Able Squad come out of the bunker. Marsh greets him, "Welcome to Chicago, Admiral." They shake hands and he replies, "It's good to be home." The final shot is of the last word remaining from the inscription over Phaeton's bunker, SPERANZA, with in English is "HOPE".