The following month, the capital fell into chaos as John Wilkes Booth assassinated President Abraham Lincoln, and Booth's co-conspirator Lewis Powell severely injured Secretary of State William H. Seward on the night of April 14, 1865. Booth died on April 26, 1865, from a gunshot wound. When the trials for the conspirators were ready to start, Bingham's old friend from Cadiz, Edwin Stanton, appointed him to serve as Assistant Judge Advocate General along with General Henry Burnett, another Assistant Judge Advocate General, and Joseph Holt, the Judge Advocate General.
The accused conspirators were George Atzerodt, David Herold, Lewis Powell (Paine), Samuel Arnold, Michael O'Laughlen, Edman Spangler, Samuel Mudd and Mary Surratt. The trial began on May 10, 1865. On June 29, 1865, the eight were found guilty for their involvement in the conspiracy to kill the president. Spangler was sentenced to six years in prison, Arnold, O'Laughlen and Mudd were sentenced to life in prison and Atzerodt, Herold, Powell and Surratt were sentenced to hang. They were executed July 7, 1865. Surratt was the first woman in American history to be executed by the Federal government of the United States. O'Laughlen died in prison in 1867. Arnold, Spangler and Mudd were pardoned by President Andrew Johnson in early 1869.