The history of the Children of Atom is tied closely to the history of Megaton. The founders of the religion were part of the refugees that took shelter in the crater in the 23rd century, worshipping the bomb that lay at its center. As the crater was settled, the zealots aided in building the walls and clearing the wreckage to make way for the future town. The fledgling religion's only condition was that the holy bomb remained undisturbed. As it seemed to be a pile of harmless scrap, the town acquiesced. The Children of Atom became a permanent element of the town and by the mid-2250s, the confessor of the church had enough clout to vouch for newcomers in Megaton. A young wastelander named Cromwell benefited from this and became a fervent adherent of the faith, eventually succeeding the confessor. By 2277, the 44-year-old Confessor Cromwell became an eccentric distraction to most of the citizens, with church attendance steadily dwindling.

However, to adherents of the faith, Cromwell was the great prophet of Atom. It is under his auspices that a group of Children of Atom departed from Megaton and traveled to the North between late 2260s and early 2270s.