Dr. Atom was an alternate version of Lex Luthor from one of the many pocket dimensions in the Archive of Worlds. His world was destroyed by Auteur.io and so he then tried to create a perfect world which their mad creator would spare.
Auteur.io deemed his world incapable of achieving perfection and destroyed it. Dr. Atom escaped and glimpsed the reality behind all realities. He learned that Auteur.io was obsessed with creating a utopia and determined that if he could create a perfect world then it would be safe. He took up residence on The World of the Knight and made contact with Martha Wayne on The World of Tomorrow. They made a deal to "perfect" the World of Tomorrow, Dr. Atom would provide Wayne with advanced technology to improve her world, which she passed off as her company's inventions; and she sent him villains from her world to both remove the criminal element and provide Atom with a ready supply of test subjects for his experiments.
As a result, The World of the Knight became ever more dark, dirty and crime-ridden. Only Gotham City was able to maintain some semblence of order due to the efforts of Batman and Robin. Lois Lane learned that Dr. Atom was behind the worlds ill's and prepared an expose on him and his secret society. Dr. Atom bombed the Daily Planet to prevent publication and Lois was presumed dead. However, she survived and spent weeks in a coma. When she awoke she became the Spider Lady and took over the criminal gangs that now ruled Metropolis. She continued to try to expose him and tried to free the inamtes from Arkham Asylum so they could reveal that their counterparts from The World of Tomorrow were being used for medical experiments. Batman foiled her plans but decided to investigate her claims, eventually following the trail to Dr. Atom's fortress in the Arctic. They fought their way through Dr. Atom's henchmen and eventually reached the "burn hole" leading to The World of Tomorrow, which the Lois Lane of the other world fell through into The World of the Knight.
Superman soon followed her through and Dr. Atom ordered them all destroyed, but Superman fought off his forces and they all escaped back to Gotham. When they re-emerged in Metropolis, Atom sent Warden Luthor and his army of mutated inmates after them, but the heroes escaped back to The World of Tomorrow. Later that night, Martha Wayne called Dr. Atom to arrange another exchange at Gotham Cemetery, where she would hand over The Unknown Wizard in exchange for a serum which would grant her son superpowers. The Unknown Wizard managed to tell Lois about the exchange and Superman, Batman and Robin arrived to capture him. Dr. Atom held Superman at bay with his Kryptonite pendant, and Martha injected Bruce with the serum, transforming him into a powerful Bizarro-like creature. Batman and Robin disarmed and captured Dr. Atom, allowing Superman to defeat Bruce.
The heroes unmasked him and were shocked to learn he was Lex Luthor, as each had fought his counterpart in their own worlds. He revealed the turth about their realities and broke free of his bonds. He ran through the burn hole with the three heroes chasing him. They emerged in the "superseding reality", to see Auteur.io fighting their counterparts. Auteur.io trapped the other Superman and Batman in a Phatom Zone crystal and then noticed his "characters", who were doll-sized in the real world. Dr. Atom told Auteur.io that he had been creating a perfect world for him, but Auteur.io crushed him in rage for telling him how to create his utopia. Dr. Atom activated a bomb built into his suit which wounded Auteur.io enough that he fled into the Archive.
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