As the organizer of internal security, Edwin M. Stanton was blamed for the assassination of Abraham Lincoln on 14th April 1865. Stanton immediately summoned Lafayette Baker, head of the National Detective Police (NDP) to Washington with the telegraphic appeal: "Come here immediately and see if you can find the murderer of the President." Baker arrived on 16th April and his first act was to send his agents into Maryland to pick up what information they could about the people involved in the assassination.

Within two days Baker had arrested Mary Surratt, Lewis Paine, George Atzerodt and Edman Spangler. He also had the names of the fellow conspirators, John Wilkes Booth and David Herold. When Baker's agents discovered had crossed the Potomac near Mathias Point on 22nd April, he sent Lieutenant Edward P. Doherty and twenty-five men from the Sixteenth New York Cavalry to capture them.

On 26th April, Doherty and his men caught up with John Wilkes Booth and David Herold on a farm owned by Richard Garrett. Doherty ordered the men to surrender. Herold came out of the barn but Booth refused and so the barn was set on fire. While this was happening one of the soldiers, Sergeant Boston Corbett, found a large crack in the barn and was able to shoot Booth in the back. His body was dragged from the barn and after being searched the soldiers recovered his leather bound diary. The bullet had punctured his spinal cord and he died in great agony two hours later. Booth's diary was handed to Lafayette Baker who later passed it onto Edwin M. Stanton. Baker was rewarded for his success by being promoted to brigadier general and receiving a substantial portion of the $100,000 reward.

On 1st May, 1865, President Andrew Johnson ordered the formation of a nine-man military commission to try the conspirators involved in the assassination of President Abraham Lincoln. It was argued by Edwin M. Stanton, the Secretary of War, that the men should be tried by a military court as Lincoln had been Commander in Chief of the army. Several members of the cabinet, including Gideon Welles (Secretary of the Navy), Edward Bates (Attorney General), Orville H. Browning (Secretary of the Interior), and Henry McCulloch (Secretaery of the Treasury), disapproved, preferring a civil trial. However, James Speed, the Attorney General, and Joseph Holt, the Advocate General of the Army, agreed with Stanton and therefore the defendants did not enjoy the advantages of a jury trial.

The trial began on 10th May, 1865. The military commission included leading generals such as David Hunter, Lewis Wallace, Robert Foster, August Kautz, Thomas Harris and Albion Howe. The Attorney General, James Speed, selected Joseph Holt and John Bingham as the government's chief prosecutors.

Mary Surratt, Lewis Paine, George Atzerodt, David Herold, Samuel Mudd, Michael O'Laughlin, Edman Spangler and Samuel Arnold were all charged with conspiring to murder Lincoln. During the trial Joseph Holt and John Bingham attempted to persuade the military commission that Jefferson Davis and the Confederate government had been involved in conspiracy.

Joseph Holt attempted to obscure the fact that there were two plots: the first to kidnap and the second to assassinate. It was important for the prosecution not to reveal the existence of a diary taken from the body of John Wilkes Booth. The diary made it clear that the assassination plan dated from 14th April. The defence surprisingly did not call for Booth's diary to be produced in court.

On 29th June, 1865 Mary Surratt, Lewis Paine, George Atzerodt, David Herold, Samuel Mudd, Michael O'Laughlin, Edman Spangler and Samuel Arnold were found guilty of being involved in the conspiracy to murder Abraham Lincoln. Surratt, Paine, Atzerodt and Herold were hanged at Washington Penitentiary on 7th July, 1865. Surratt, who was expected to be reprieved, was the first woman in American history to be executed.

The decision to hold a military court received further criticism when John Surratt, who faced a civil trial in 1867, was not convicted by the jury. Michael O'Laughlin died in prison but Samuel Mudd, Edman Spangler and Samuel Arnold were all pardoned by President Andrew Johnson in 1869.