No case in which Johnston was involved was more heartbreaking or controversial than the Branch Davidian incident which took place east of Waco, Texas. Johnston helped write the federal search warrant for the Davidian Compound and listened over police radio channels as machine-gun fire break out on the morning of February 28, 1993. Johnston called in the Texas Rangers as an independent investigative body to look into what happened which lead to the deaths of four federal agents, the wounding of 15 more, and the eventual death of eighty Branch Davidian sect members.
Attorney General Janet Reno selected Johnston as one of five federal prosecutors who would pursue the case in court. For two months, a controversial jury trial took place in San Antonio, Texas. At the end, nine of the twelve Branch Davidians were convicted of a federal offense.
Following the trial, the controversy continued. Johnston allowed an independent film maker to see physical evidence seized from the Davidian Compound. Allegations were made against the FBI regarding munitions fired at the Compound, and formal allegations were brought against Johnston for his handling of the matter. Johnston testified before Congress regarding the investigation and many books, articles, and programs have been produced about the matter. Johnston gave a lengthy interview to Dan Rather of 60 Minutes regarding the case.