Superman, Hawkgirl, and J'onn are pulled into the asteroid by Brainiac's tractor beam. Within the asteroid, they enter a huge chamber and are taken to a vast computer control center where Brainiac awaits them. He offers Superman the chance to join him in perpetuating Krypton by continuing its legacy, but Superman refuses. Brainiac boasts that all that is left of Krypton, resides within him, but Superman insists that he's a perversion of the true Krypton. Brainiac attacks and stuns Superman and J'onn, but Hawkgirl smashes him apart. However, dozens of Brainiac drone shells enter, all informing the heroes that the fight is not over.
On New Genesis, Highfather is teaching the children when Orion brings batman and Wonder Woman to him. Orion wants to launch an attack and end the war between Apokolips and New Genesis for good, but Wonder Woman wants a more peaceful solution and insists that Superman does as well. Highfather warns that he made a pact with Darkseid to keep the peace, and goes to commune with the Source wall. Angry, Orion walks away.
The heroes manage to defeat the first wave of Brainiac drones. However, a boom tube opens and Darkseid steps through... to blast the heroes down. He smashes Hawkgirl and J'onn deep into the planet's core, and then tells Brainiac that he has fulfilled their bargain and given Superman to the computer villain.
Orion is eager to begin the final battle, unconcerned with the fatalities that might occur among the "Bugs" of New Genesis. When Wonder Woman tries to stop him, he ignores her and summons a boom tube. He teleports away and they enter the tube to follow him.
Brainiac fastens Superman into his machinery. Darkseid reminds him of his promise to spare Apokolips in return for Superman, and then wonders why Brainiac wants petty vengeance. The computer villain explains that he has reached the limits of his programming. To continue his evolution, he needs to tap into and duplicate Kryptonian DNA, and Superman is the last Kryptonian. He begins to extract Superman's DNA, but Darkseid sabotages the control mechanisms and takes control of Brainiac.
Recovering consciousness, Hawkgirl flies J'onn back up to the control chamber. Once he wakes up, they go after Superman and fly through the databanks. J'onn suggests that they use the information to find Thanagar, but Hawkgirl hastily says that they need to concentrate on saving Superman.
Superman wakes up and Darkseid explains that he has betrayed Brainiac so that he can use Brainiac to access the Anti-Life Equation and take control of the universe, recreating it in his image.
Orion provides protection from outer space to Batman and Wonder Woman, and follows a nearby energy trail to the asteroid.
On New Genesis, the energy vortex from Darkseid's efforts forms above the planet. Highfather tells Lightray to get all of the city's residents into the escape pods and flee.
Brainiac warns Darkseid that his efforts are causing an energy overload. Darkseid ignores him and is then knocked back as Hawkgirl arrives and attacks him with her mace. She and J'onn try to free Superman, but Darkseid orders Brainiac to attack them with his drones. The drones knock out Hawkgirl, sending her plummeting several stories. J'onn grabs one of the drones and then turns its wrist-blasters against the others. They prepare to overwhelm him, but Orion arrives and attacks Darkseid, while batman and Wonder Woman defeat the drones and rescue Hawkgirl.
On the surface of New Genesis, Forager watches as the residents of New Genesis flee the floating city.
While Darkseid fights his son, Batman frees Superman. Without Superman as a power source, the system collapses and the asteroid begins to destroy itself. Batman tells everyone to get out, but Superman ignores him and goes after Darkseid.
In a corridor, Darkseid crushes Orion and prepares to leave, but Superman arrives and attacks him. The Man of Steel warns informs Darkseid that he won't be leaving. When Darkseid tries to use Orion's Mother Box to create a boom tube and escape, Superman destroys it and attacks.
As they get out of the asteroids, the League members realize that Superman has stayed behind and Batman goes to get him.
Darkseid initially overwhelms Superman, but the Man of Steel rallies and smashes the villain down. Superman prepares to kill Darkseid, but Batman arrives and warns that they only have seconds left until the asteroid destroys itself. Superman ignores him, leaving Batman no choice but to grab him and teleport them and Orion away via boom tube. Sneering, Darkseid declares Superman a loser... just as the asteroid blows up.
On New Genesis, Batman tries to reassure Superman, insisting that Darkseid couldn't have survived the explosion. Superman angrily insists that Batman isn't always right. Highfather tends to Orion, his adopted son, and Lightray warns that the other evacuees have disappeared. Forager comes out of the woods, bringing the other city residents with him. When they landed on the planet, Forager and his people got them to safety. He apologizes, but Highfather says that he's the one who owes the mere "Bug" an apology for his attitude. He tells Forager that he has found a place among the gods. J'onn and Hawkgirl listen, and J'onn tells her that someday she will find her place as well, and Hawkgirl considers the possibility.