"Alas, Babylon" is the secret message that Mark gives Randy to warn him of the impending nuclear attack:
"I won't call you up and say, 'Hey, Randy, the Russians are about to attack us.' Phones aren't secure [...] But if you here 'Alas, Babylon,' you'll know that's it'" (17).
The distinct code words comes from Randy and Mark's boyhood when they use to sneak down to the Afro-Repose Baptist Church on "Sunday nights to hear Preacher Henry calling down hell-fire and damnation on the sinners in the big cities. [...] It seemed that he ended every lurid verse with, 'Alas, Babylon!'" (14). Since then, the two brothers used the phrase to describe any calamity or disaster. When Mark feared the sudden approach of nuclear war, he told Randy that he would use that phrase from the Bible to warn him of a possible strike.
The phrase certainly reflects one of the larger themes of the novel, destruction of civilization, carrying with it the connotation of punishment for an immoral society. "Alas, Babylon" is Randy's first sign of the nuclear attack, and the Biblical allusion to the city of Babylon, which was "burned off the face of the earth in an hour" shares many similarities to the horrific destruction of the cities that will be destroyed in the coming nuclear Armageddon (15).