Atom has been requested by a hospital to help deal with a complicated brain surgery. A small boy has a tumour in his brain and will die if not operated within a few hours. Atom reduces himself to sub-microscopic size and goes in through the boy's retina into his brain. There he is surprised to find a bacterial infection, which has recently taken the form of a burgeoning civilization.
Atom comes back to the Justice League headquarters on the moon and explains the developments. The bacteria are mining the boy's brain's dendrite material for harnessing energy. He makes plans with Superman, Green Lantern, Flash and Wonder Woman to go inside the boy's brain and stop the infection. They go back to the hospital and get into the boy's brain by using advanced size-reduction belts developed by Atom. Once they reach the civilization, they are taken to the headquarters by an army.
There Superman tries to reason with the king bacterium to halt the progress. He warns them that the doctors are holding off a laser surgery, which could prove destructive to the civilization. The king does not believe a word and tries to imprison the JLA. The JLA try to counter-attack but find their powers drastically diminished. They are imprisoned, and Superman is taken away for interrogation.
Atom explains to the others that their abilities are not working because of their size reduction. He says that any call for help to the outside world will be of no use either. Jom-ft-vom, a council member of the bacteria hands his resignation and helps Superman to escape. He says that despite his warnings, the other leaders are not heeding his theories of the outside world. Superman and Jom-ft-vom free the JLA and they make their way to the main power station. Here they find that a riot has started, and it has damaged the stimulating gland. Soon there is a massive explosion and the power station goes up in flames. Atom warns them that the surgical laser will automatically activate and bear down upon them in approximately 90 minutes.
The JLA start evacuating the town. Jom-ft-vom knows well that they will not survive. He and his pair, Li-tam, place their DNA within a space-capsule and launch it. The 90 minutes are up. The laser cuts in from the sky and blows up the town. The JLA, except Superman, comes out of the boy's brain.
The boy survives. Sometime later, Superman comes out and tells him all about the bacteria. He adds that not a single one had survived. But he still hopes that the bacteria's space-capsule has landed somewhere else inside his body.