Part 2 begins 600 years later, in a courtroom in the territory of Texarkana. A man named Hannegan II is the mayor. Marcus Apollo is the Pope’s ambassador. During a party in the courtroom, he realizes that war is coming with the nomadic clans who live on the Plains. Hannegan’s courier—a man named Sarkal—returns, alive, from the camp of a warlord named Mad Bear. Mad Bear would never have left an enemy alive, so Apollo assumes the courier didn’t actually relay the message.

Apollo talks with Brother Claret and then the scholar Thon Taddeo, who wants to discuss the Leibowitz documents. He wants to see them but would prefer that monks bring the documents to him rather than make the dangerous trip himself. They agree to talk more that night. Apollo knows that Taddeo is related to Hannegan and, therefore, must be treated respectfully. Apollo says that Claret must visit the Vatican to discuss the war that Hannegan is fomenting under the guise of uniting the continent.

Later, Taddeo visits Apollo’s study. Taddeo says no one believes in the documents, but there must be an investigation. Taddeo is an eminent scholar and a genius. He thinks the documents could be from science textbooks and wishes to judge for himself.