Weitzel soon established his headquarters in the home of Jefferson Davis. His aide, Lieutenant Johnston de Peyster, is credited with raising the first U.S. flag over the city after its capture by the Union. The next day, President Abraham Lincoln visited the Confederacy's capital. Weitzel served as Lincoln's confidential aide and bodyguard during two days of peace negotiations with Confederate representatives. After Lincoln's assassination days later, Secretary of War Edwin M. Stanton refused to believe the generous terms on which Lincoln would have allowed Virginia to rejoin the Union.