The story begins in the future. A video shows the JLA going toe-to-toe against Luthor's villains. A devastating battle ensues and many on both sides are killed. Superman returns from exile and starts battling Luthor, but is a victim to Luthor's ruse, and is weakened by kryptonite. Luthor thrusts a kryptonite spear into Superman's heart.
Lex Luthor has finally killed Superman. He has defeated the JLA and most of the other heroes are either dead or beaten. Just as Luthor begins to gloat it is revealed that he had made some sort of deal with Brainiac, Luthor would help Brainiac defeat Superman, and in turn Brainiac would leave Earth alone for Luthor to rule as he seemed fit.
Brainiac then reveals to Luthor that he had never planned to let the Earth survive. Luthor has served his purpose and now he will be kept as a trophy for his great IQ. Brainiac takes over Luthor's battle suit and strats to use Luthor's own tech against him and his allies. Brainiac in truth is stealing and collecting all of Earth meta-human powers and abilities. Brainiac unleashes his exobytes over the world, and also activates the robots that Luthor had been building for him over the past few years.
Luthor finds a dying Black Adam, and coaxes him to utter "SHAZAM", one last time, while standing in close proximity to him. The lightning destroys Braniac's control units in Luthor's armor. Luthor then uses a last ditch effort to get to a secret command bunker in New Mexico. There he communicates with all remaining meta-humans and pleads with them to join him against Brainiac.
The Atom is the first to respond. With his help, four hours later Luthor has his 'motliest group of champions that the human race has ever been forced to relay on". They include both heroes and villains.