The Javelin is pulled into the asteroid and they have no choice but to wait. They are drawn into a huge chamber and a hover platform invites them to board it. When they do, it takes them to another chamber and Brianiac emerges to greet them. He offers Superman another chance to join him in carrying on the legacy of Krypton, an offer which Superman refuses. The computer explains that everything that remains of Krypton is stored with him, but Superman dismisses him as a perversion. Brainiac has his drones open fire and the three heroes quickly destroy them. Brainiac himself attacks Superman and J'onn, shocking them, but Hawkgirl smashes him down. She assumes it's over, but a dozen Brainiac drones enter and warn them that it's nowhere close to finished.
Highfather is supervising the children of New Genesis as they work their gardens. Orion arrives with Batman, Wonder Woman, and Lightray, and informs his adopted father that they have news of Apokolips. Orion insists that it is time to end the war between the two worlds and launch an attack. Wonder Woman warns that Superman doesn't want a war, and Highfather says that they swore a pact to maintain the peace. He goes to commune with the Source and seek wisdom, and Orion angrily stalks off.
The heroes defeat the next wave of Brainiacs, but are stricken down when a new player arrives: Darkseid, working in conjunction with Brainiac. He blasts J'onn and Hawkgirl down into the floor and assures Brainiac that per their arrangement, he's delivered Superman into his hands.
As Orion prepares for war, he dismisses the dwellers below as mere bugs. When he prepares to leave, Wonder Woman wonders why he's so eager for war. He ignores her advice, creates a Boom Tube, and teleports away before they can stop him. They leap into the Boom Tube after him.
Brainiac transports the unconscious Superman to a chamber filled with Brainiac drones. Darkseid reminds him that he agreed to spare his planet in return for delivering Superman. When he asks why Brainiac needs Superman, Brainiac explains that he is has reached the limits of his programmed function. To evolve to the next level, he will extra living DNA from the last Kryptonian. He fastens Superman into a device and extracts the necessary material. As he proceeds, Darkseid secretly attaches a device to the consoles. Energy surges through the machines, allowing Darkseid to take control of Brainiac's control mechanisms.
Hawkgirl pulls J'onn back to the chamber and wakes him up. They realize that Superman was right and fly off to find him. As they go through Brainiac's processing core, J'onn suggests that they may contain information on Thanagar, Hawkgirl's homeworld. She brusquely says that there's no time to look and they need to find Superman.
Superman recovers consciousness and asks Darkseid why he's betraying his ally. The lord of Apokolips explains that he plans to gather the energy necessary to solve the Anti-Life Equation.
Orion, Batman, and Wonder Woman follow Darkside's trail to Brainiac's asteroid. Inside, Darkseid explains that he plans to use the Anti-Life Equation to recreate the universe in his image.
On New Genesis, Highfather's musings are interrupted when a vast energy void opens above the planet, pulling everything into it. Highfather orders Lightray to order everyone into the escape pods and evacuate the city.
The captive Brainiac warns that the process is reaching critical mass, but Darkseid satisfied things are going according to plan. Hawkgirl arrives to attack Darkseid and then tries to free Superman with J'onn's help. Darkseid forces Brainiac to send his drones against them. Hawkgirl is blasted unconscious but J'onn smashes a drone preparing to kill her, and then uses its weaponry against the others. Orion arrives to destroy the drones and attack his father. Wonder Woman and Batman defeat the remaining drones and gather the unconscious Hawkgirl.
The escape pods leave the New Genesis city, while on the surface below, Forager watches as the gods are cast down.
Orion and Darkseid battle while Batman destroys the control system and frees Superman. With the circuit incomplete, the system fails. Batman says they need to leave as the complex explodes, but Superman turns and seeks out his enemy.
Darkseid smashes Orion down but Superman arrives to block his escape. He informs Darkseid that he won't be going anyway, destroys Orion's Mother Box to prevent him from teleporting away, and informs him that this time he won't stop until Darkseid is destroyed. Darkseid smashes him down.
The heroes realize that Superman has gone back, and Batman goes to get him.
Superman rallies and smashes Darkseid back, punching him repeatedly. His final blows sends Darkseid flying back down the corridor. As Superman moves in, Batman arrives and tells him that they need to go. Superman shoves him away and tells him to leave, but Batman grabs him and teleports away via a Boom Tube, pulling in Orion as well. Darkseid smirks in triumphant... and the asteroid blows up.
On New Genesis, Batman tries to assure Superman that Darkseid couldn't have survived. Superman angrily tells him that he isn't always right. Meanwhile, Highfather tends to the wounded Orion, while Lightray returns and tells him that the other evacuees are lost. However, Forager emerges from the woods with the rest of the the city dwellers, including the children. They explain that Forager hid them until the storm was over. Forager begs his forgiveness, but Highfather asks his apologies for overlooking him. He assures the valiant Bug that he has found his place among them. Listening, J'onn tells Hawkgirl that someday, she might find her place. She admits it might occur.
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