When Abraham Lincoln was assassinated in April, 1865, Holt joined Edwin M. Stanton, Secretary of War and James Speed, the Attorney General, in calling for the conspirators to be tried by the military commission. The new president, Andrew Johnson, agreed and ordered the formation of a nine-man military commission. This included Howe, David Hunter, Robert Foster, August Kautz,, Lewis Wallace and Thomas Harris. 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 the chief prosecutor, Joseph Holt, attempted to persuade the military commission that Jefferson Davis and the Confederate government had been involved in conspiracy.
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.
After the was Howe became Colonel of the 4th United States Army. Albion Howe died in 1897.