Atom assists during a surgery to remove a little child’s brain tumour. But he discovers the tumour is a whole civilisation of bacteria which have their own industry and, thus, are polluting the brain of the young boy. Before this civilisation gets wiped out by laser surgery, Atom invites members of the JLA to join him in convincing the bacteria to stop destroying their environment and save their lives in the process as well.
In their miniaturised state, Atom and the JLA try to negotiate with the bacteria’s leaders, but they do not believe their story and take the heroes into custody. This is possible because in this microscopic state the powers of the JLA do not work properly. While Superman is getting tortured, Atom hopes the JLA’s powers will return after their bodies got more accustomed to the situation. Thankfully, one of the bacteria’s scientists takes side with the JLA. He sets the heroes free and organises a riot resulting in the destruction of the power plant. Atom realizes that the boy’s doctors now will start the laser surgery, so they need to evacuate the microbe city quickly. The JLA succeeds, but after they have left the boy’s brain, his immune system wipes out all bacteria anyways. But perhaps, some of them still found a way to survive.