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Desaad and Granny Goodness overlook the chaotic ruins of Apokalips and beyond the great statue of Darkseid: the planet has been ravaged after its split with its sister planet New Genesis. Granny insinuates that Desaad, Darkseid's "most loyal follower," was somehow responsible for Darkseid's becoming one with the Source Wall. Desaad prepares to strike Granny down for defiling his good name and spirit, but is knocked unconscious by Kanto, Darkseid's finest assassin and loyal student of Granny. He points to the skies over Apokalips, and shows Granny the real threat; it's not the now-sleeping Desaad, but the warships of Virman Vundabar, which bombard the surface of the dark planet.
As Desaad awakens, he directs the para-demons to attack Vundabar's airfleet. A bloody battle ensues, and the casualties quickly rise. Kanto proposes that Desaad use what Vundabar does not possess; the strongest weapon there is on Apokalips; and a weapon Desaad knows how to handle oh so well: fear. Granny loans him a new aircraft, which Desaad pilots and uses to break apart Vundabar's fleet. Desaad uses it to tears into Vundabar's command ship and fend off the dictator-to-be's legions of troops.
But below, on the planet's surface, the great statue of Darkseid somehow stirs. Suddenly, and almost inexplicably, it comes to life. Grabbing Vundabar's command ship and crushing it into dust, the giant icon of the planet's departed master is alive, with the spirit of Darkseid reaching out from the Source. Darkseid scolds his bickering minions, and directs their anger and hatred not towards each other, but towards the gods of New Genesis, which sits ravaged yet undisturbed in the night's sky. The statue falls silent, and Darkseid speaks no more to his . His elite gather, and reconcile, now ready to renew their deadly efforts towards the beings of New Genesis. And Kanto, the ever-loyal assassin, reminds his comrades that Darkseid's power has been grandly defined, and he knows that Darkseid won't hesitate to use it again...
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The evil Neron, lord of the underworld, spreads his scheming to Apokalips, which is in disarray after the latest "death" of its dark lord Darkseid. He offers several of Darkseid's Elite (Granny Goodness, Desaad, Dr. Bedlam and Virman Vundabar) powers of unimaginable description. But he also sets them up against each other, in order to see Apokalips tear itself apart . The lowly Hunger Dogs, whispering the rumors of Darkseid's demise, begin to uprise, and soon all of Apokalips is engaged in a bloody battle. All because of a few deals with the Devil. But Desaad ends the chaos, disguised as Darkseid, quieting the crowds and restoring what order Apokalips has ever known. Neron declares himself the only victor of this battle, claiming that despite his offerings of power, the greed of Darkseid's minions to stab each other in the back led only to this bloodshed, not him.
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After the latest "invasion" of Supertown by the hungry bugs of New Genesis, Highfather, the leader of the New Gods of New Genesis, reminds his son Orion, who used much force to stop these bugs, that all life on New Genesis is sacred, and the bugs are no exception. Metron appears after Orion and Lightray leave, and asks Highfather about more secret matters: like the "pact," which forced Highfather to trade his son to Darkseid in return for Orion, and for peace between their worlds; Highfather has never been able to tell Orion this truth, nor has he ever stopped wondering what has happened to his true son, now on Apokalips.
On Apokalips, Scott Free, Highfather's son, is a warrior-in-training, who possesses a spirit which defies that world's dark master. As well as a boom tube generator, which he stole from Darkseid's labs. After outrunning a pack of parademons, he is caught by Barda, one of Darkseid's Furies, who "graciously" lets him go after Scott spins a few lies together into an alibi. In Darkseid's chambers, Desaad informs his master that Free has escaped with a generator, but Darkseid dismisses this, presenting his minion with an even greater sight: his "Superman," the Kryptonian child, whom Darkseid has molded to be his finest warrior. He debuts his achievement in a gladiator battle against Kalibak, his brutish son. Donned with an almost-invincible armor, Superman arises from the fire pits and fights Kalibak. All look on with awe as, after a thorough beating, Superman defeats Kalibak, and at Darkseid's command, kills him.
Scott Free, among the many who watch this, has finally had enough of Apokalips and its evil ways, and, after saying farewell to his "teacher" Himon, leaves with the intent of activating his new boom tube generator and abandoning Apokalips forever. But not before the Superman finds him. Scott tries to fight back, but Superman defends himself, paralyzing his prey in the process. Scott manages to activate the generator and escape both Apokalips and death by Superman. Superman apologizes to Darkseid for failing him, but is instead presented with a even greater task: destroying New Genesis. Now that the "pact" has been broken, thanks to Scott Free's escape, Darkseid instructs Superman to lead an army to New Genesis and plant a powerful omega warhead in the planet's core. The armies of Darkseid attack Supertown and the New Gods, and Superman completes his task; upon the warhead's detonation, the beautiful world of New Genesis is ravaged and incinerated. Superman joins the forces on Supertown, and discover that all of the New Gods, save Highfather, have magically disappeared. Superman confronts Highfather, and they magically disappear too. But Highfather transports himself and Superman to the Source wall on New Genesis, where the "Uni-Friend" writes: The war will end when destroyer becomes creator. Highfather then uses his powers to reveal the truth of Superman's past to him: he is not Darkseid's son, but a child from the planet Krypton, brought to Apokalips only through Darkseid's interference. As Highfather joins the Source, he uses his final powers to transport Superman to Earth, where a local woman, named Lois, finds the warrior floating in a river.
Darkseid travels to New Genesis to see his victory first-hand. He learns that Superman is gone, probably caught in the omega warhead blast, and shows pity only because he has lost a valuable tool of destruction. He then realizes what happened to all the New Gods who simply "disappeared:" Highfather sent them to Earth.
Back on Apokalips, Metron stumbles across Darkseid, who reveals to the New God that a processing unit in Superman's Kryptonian craft, which had been mysteriously removed years before but recreated by Darkseid since, held the information that Superman himself holds the solution to the anti-life equation, which Darkseid has strived for ages to solve and control, within his genetic code. Metron admits his actions, declaring that the equation is too much power for one being to possess; Darkseid responds by destroying Metron for his deception. On Earth, the S.C.U. tries to analyze the Intergang weapons, when Lex Luthor, the head of S.T.A.R. Labs, arrives, showing them the corpse of a dead parademon, hinting that the demon and the weapons are both part of some alien invasion of Earth. Superman, with Bibbo and Jimmy, save a doctor from a buring clinic in Suicide Slum. Superman confronts a parademon, having just killed Fastbak the New God, and kills him when the trooper tries to kill the human doctor. He finds Fastbak's Mother Box, and, after an encounter with Lois Lane, who herself is curious about the alien presence in Metropolis, intends to find these New Gods on Earth. They succeed in finding them on an abandoned island in the harbor, just as Barda, sent by Darkseid to locate the New Gods, also finds Superman. Orion is enraged to see that the man who destroyed New Genesis still lives. The Mother Box Superman carries protects him from Orion's attack, then adapts Superman's armor to possess its power. The New Gods promptly retreat, seeking a new refuge in Metropolis. Despite Lois' pleas, Superman agrees to go back to Apokalips. Barda reports to Darkseid that the New Gods are on Earth, and that Superman is also alive: he is pleased.
Meanwhile, Lex Luthor introduces Lois to his source of knowledge on the New Gods problem: Scott Free, now completely paralyzed due to even more injuries sustained upon his arrival on Earth. He discovers Superman is now in Metropolis, and uses Luthor's equipment to find, capture and imprison Darkseid's warrior. Just as he is imprisoned, Darkseid arrives. He disposes of the toadying Luthor, who is sent to Apokalips to be Granny Goodness's newest plaything, and offers Scott the Mobius chair in exchange for Superman. Scott Free agrees, and Superman is returned to Apokalips, where Darkseid begins to extract the secrets of the anti-life equation from him. The equation is completed, and Darkseid instructs his forces to take over Earth, which he will then enslave with the power of the anti-life equation.
He finds the New Gods on Earth, who realize that he is no longer Darkseid's minion, and together they attack Darkseid's forces. As the New Gods fight Darkseid's legions, Superman goes after Darkseid himself. But Darkseid shows Superman that the New Gods are no threat to him, as their numbers begin to diminish. Superman is downed, but not destroyed, by Darkseid's Omega beams as he heads off to destroy the transmitter. Suddenly, Orion returns, with the bug armies alongside him, and attack the anti-life transmitter themselves. Within minutes, Darkseid's transmitter is destroyed, and . Darkseid unleashs an "anit-mother box," which destroys Orion's Mother Box and Superman's Mother Box-enhanced armor. As Orion lays dying, Superman fights on, but is time and time again laid low by Darkseid's power. Scott Free returns, having seen what lies beyond, and agrees to help. He has Lightray instill some of his light powers within Superman, to give the Kryptonian even more power. Lightray, about to give Superman even more power, is killed by Dr. Bedlam, who in turn is imprisoned in an energy cube by Scott Free. In his dying moments, Lightray uses the rest of his life-force to empower Superman, which works, and Superman defeats the evil Darkseid with one mighty blow. His evil soul is committed back to the Source, and the final pieces of Darkseid's occupation begin to scatter and disappear. Scott Free leaves Orion and Superman to rebuild that which has been ravaged by Darkseid, hoping their lives are not so chaotic ever again...
One year later...
Metropolis is once again a magnificent city, recovered from the chaos Darkseid brought. The New Gods now reside on a new Supertown, a place where both New God and human are welcome, hovering over Metropolis. Meanwhile, on Apokalips, Superman destroys the remnants of Armagetto, bringing life to a once-dead planet. As Apokalips begins to show signs of life again, Superman and Barda plan to do the same for New Genesis.
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