The Justice League confront the villains and Lex explains how they escaped Darkseid's attack and then knocked out Lightray of New Genesis to return to Earth. Superman is reluctant to accept the villains' help but they're interrupted when Darkseid launches simultaneous attacks across the globe via Boom Tube. The Justice League mobilizes and the villains insist on helping out. Superman agrees but Lex warns it'll be back to business-as-usual after they thwart Darkseid.
Superman is beamed to Darkseid's flagship over Metropolis while the parademons launch their attack. Heroes and villains alike repel the invasion force across the globe while Superman, Batman, and Lex Luthor appear in Metropolis via teleporter. They easily dispatch the first wave of parademons and Darkseid descends to make his entrance and vows to crush Superman.
Lex attacks Darkseid first to gain revenge for Darkseid destroying Brainiac, but Darkseid casually throws him off the building and Batman manages to rescue him. Darkseid grabs the Daily Planet globe and begins the fight, sending Superman plunging down through the floors. Meanwhile Darkseid sets up magma-tappers across the globe to create firepits and create Apokolips on Earth. Mr. Terrific directs the forces against the magma-tappers and in Washington, Hawkgirl goes down with a spear in her back. Steel buys her enough time to use her mace and destroy the magma-tapper there.
In Paris, the Flash creates a trench while Green Lantern catapults the drill into an enemy ship. In Metropolis, Darkseid has the upper hand but Batman and Lex return to distract him. The parademons go after them but Superman has recovered and begins fighting, while the New God Metron hovers overhead.
In China, an elderly man comes up to help and reveals that he is...J'onn J'onzz in disguise. Lex and Batman fight back-to-back while Superman is knocked down and Batman rescues him once more. Darkseid unleashes the Omega Effect and Batman manages to dodge it and Lex runs. Darkseid continues to beat Superman into unconsciousness then slams him down on his knee.
Lex sees Metron and demands help from him. Metron notes there is one thing that might destroy Darkseid and takes Lex to it. Batman double-teams Darkseid to let Superman get his breath and cut loose, slamming Darkseid repeatedly around the city. But it's still not enough as Darkseid unleashes the Agony Matrix on Superman.
Metron takes Lex to the Source Wall and warns him that only a 12th level intellect can survive what he's to experience. Lex is undaunted and leaps into the Wall. Darkseid prepares to kill Superman by carving out his heart with a laser-blade. Lex arrives in his business suit to show Darkseid the one thing he wants – the Anti-Life Equation. Darkseid takes it and admires its beauty. Batman gets Superman away while the Equation bursts into light and there's nothing left but a huge crater. Darkseid's force retreat while the heroes and villains assemble.
The heroes wonder if Darkseid and Luthor are dead but nobody really believes it. Batman gives the villains a five-minute head start in return for their help. At the end , the League (including J'onn) charges out, united once more against any and all threats.