The Justice League find that a deceased Scarecrow's fear toxins, a submarine, and an atomic bomb, were all stolen. They find Joker responsible, and the nuke in the center of Metropolis.
Superman enters the submarine and is hit with the fear toxins, resulting in him noticing Doomsday, and launching what he thinks is Doomsday into space.
The Justice League realize Joker's plan but are too late to stop it. When Superman launched Doomsday into space, the real person he destroyed, was Lois. The bomb, which is set to explode at the permanent end of Lois Lane's heartbeat, explodes and destroys Metropolis in a blaze of nuclear hellfire.
Superman, out of fear of realizing what happened, kills Joker by punching him through his chest, while Batman is interrogating Joker on where he got the nuke.
Superman relates all conflicts to his own tragedy and learns about violence ruining too many lives all the time. He decides to put a stop to this.
After five years since Metropolis's nuclear demise, Superman has officially united the entire Earth under his state, the One Earth Regime, and has eliminated crime and blacklisted free speech, nukes, and resistance.
Lex Luthor works with Batman on getting a Motherbox to install a machine that could get the Justice League of an alternate world(where Joker's plan backfired) into their own, to end the Regime for good. It works, but the Batman and Joker of that realm are also transported and separated and captured by regime forces.