When the Source initiated the demise of the Fourth World and the Death of the New Gods, it did so on one mistaken assumption: that extinction would end the animosity between the New Gods of Apokolips and New Genesis. The New Gods resumed their war in heaven, a war that ultimately ended when the forces of evil gained control of the Anti-Life Equation which can destroy free will. With this, Darkseid, the Dread Lord of Apokolips and God of Evil, finally achieved his ultimate goal, and in his victory, the survivors on both sides fell through reality, landing on New Earth just before the Infinite Crisis. From here, Darkseid consolidated his position, possessing a mobster named Boss Dark Side and uniting the evil gods of the Fourth World. The good gods could not fight him.
Building his position, Darkseid began using his godly power to alter reality, subtly removing the positive effects of the Fourth Worlds: as a result, Bruno Mannheim founded a cult dedicated to the evil of the Fourth World. Metron, a scientist connected to the Fourth World, fought Darkseid's actions across time and space: convincing "Mister Miracle", an escape artist, to take the role of the spirit of freedom; inspiring Anthro with "fire and knowledge". But it was not enough - Darkseid's evil was spreading over the universe like a shadow.
After the villains escaped from the prison planet, Darkseid sent Libra to lead them in the preaching of his word. Taking control of the Secret Society of Super-Villains, he transformed it into something resembling a terrorist organization. When the time was right, Darkseid arranged the death of Orion. It was only then that the heroes of Earth realised that something might be amiss. As their leading lights were picked off, the heroes united to fight them... but it was too late. Darkseid's followers spread the Anti-Life Equation across the world, taking control of everything, while at the same time taking possession of Dan Turpin. Earth itself became a doomsday singularity, a black hole corrupting time and space, where several weeks transpired inside in the matter of a few days. Worse, because the Multiverse rested upon New Earth's survival, Darkseid's presence was destroying space and time around him, which could in turn destroy the multiverse. However, there is one hero no-one could have predicted... Barry Allen, the second Flash.
At the same time, Superman, along with a number of alternate "Supermen", was called away to help the Monitors deal with the threat of Monitor Dax Novu, a fallen monitor who had become Mandrakk the Dark Monitor. To his horror, Superman discovered that Mandrakk's fall was because he had fully embraced his nature: the Monitors were celestial parasites who fed off the Bleed, and Mandrakk sought to feed off the multiverse itself. Superman was able to defeat Mandrakk, but Monitor Rox Ogama, who had conspired with Mandrakk and banished Monitor Nix Uotan to Earth, simply assumed his mantle. Superman dispatched Captain Marvel of Earth-5 to gather all the Supermen of the 52 to form a force which would be able to defeat Mandrakk. Superman was then called by the Legion of Super-Heroes to deal with Superboy-Prime, but the Legion were unable to return Superman to his time period until after Darkseid's rebirth. Recognizing that a desperate course was needed to deal with Darkseid, Brainiac 5 showed Superman schematics for the Miracle Machine.
On an Earth overwhelmed, the last remaining superheroes worked with Checkmate to try to turn the tide against Darkseid. Although they made progress in the battle of Bludhaven, Darkseid assumed full control over the people enslaved by the Anti-Life Equation. In his dungeons, Nix Uotan remembered the name of his lost lover, Weeja Dell, restoring his monitor powers, while Metron, also a prisoner, reactivated his Mother Box. Learning of Darkseid's presence on Earth, the Guardians of the Universe sent a team of Green Lanterns under Hal Jordan to eliminate Darkseid.
However, Darkseid had underestimated the resolve of Batman. Recognizing Darkseid's existence as a threat, Batman made a once-in-a-lifetime exception and used a gun to fire the radion bullet Darkseid had used to kill Orion. Darkseid was hit with the radion bullet, but not before he unleashed the Omega Sanction, the "death that is life", upon Batman. Superman then returned to New Earth, breaking through Darkseid's forces and finding what appeared to be Batman's corpse. As Darkseid mocked his old enemy and fired the bullet that killed Orion, Barry Allen and Wally West lead the Black Racer to Darkseid, who removed his soul from Dan Turpin. Superman allied with the Secret Society under Lex Luthor and Doctor Sivana, managing to break the Anti-Life Equation's hold over Wonder Woman, who in turn bound Darkseid's corpse with the Lasso of Truth, breaking the Equation's hold over the people of Earth.
Forced to miniaturize and place the people of Earth into cryogenic stasis, Superman set about building a Miracle Machine to reverse the damage done by Darkseid. Once it is complete, Darkseid makes a last ditch attempt to defeat Superman and claim the Miracle Machine. However, Superman sang a note at a frequency that countered Darkseid's own vibrational frequency, shattering his essence. Superman then needed a sample of Element X to power the Miracle Machine, and planned to make a sample using Metron's Mobius Chair. Mandrakk then returned to take his revenge as Superman used the solar energy in his body to power the Chair. Before Mandrakk could react, the Supermen appeared to hold him off while Nix Uotan restores the humanity and powers of the Zoo Crew (then trapped as ordinary animals) to be reinforcements. Hal Jordan and the Green Lanterns arrived and, with the last of their power, killed Mandrakk. Superman then used the Miracle Machine to restore Earth to its normal place in the multiverse. Recognizing that he and his fellow monitors were too dangerous to be allowed to continue, Nix Uotan banished himself and his kind throughout the multiverse, again separating himself from Weeja Dell. As Earth began the long process of recovery, the people of Earth were left with the knowledge of the multiverse.