First, no doubt assisted by his friend (and boss) Secretary of War Stanton, Holt had chosen the seven generals and two colonels who would sit as the commission members. All were Unionists who owed their commissions as officers to the president and who presumably felt a strong personal loyalty to him. These men were unlikely to develop any sympathy for the conspirators, much less consider acquitting them. In any event, there was no "presumption of innocence" at a military commission.

Second, because the charge of conspiracy leveled against Mary Surratt and her seven co-conspirators included claims that the leaders of the Confederacy were involved in the plot to kill Lincoln, Holt and his assistants introduced much evidence that had nothing to do with Surratt or the seven defendants. For example, the military commission heard testimony that Confederate agents had plotted to infect Northern cities with small-pox infected blankets and that Union prisoners had been mistreated at Andersonville prison.

Third, Holt used both direct evidence (for example, the testimony of Lloyd that Mary had come to him on the afternoon of the assassination and told him to get the 'shooting irons' ready) and circumstantial evidence (for example, that Mary ran the boarding house that hatched the conspiracy to kill Lincoln) to put together a very strong case against her. Her guilt was a foregone conclusion -- the only question was whether she would hang for her part in the conspiracy.

At the end of a two-day deliberation, the commission voted to hang Mary Surratt. At the same time, five members signed a petition requesting that President Johnson commute Mary's sentence. What happened to this petition continues to be controversial. General Holt insisted that he delivered the clemency petition to Johnson -- and that the president rejected it. Johnson later denied having seen it. But this claim by Andrew Johnson seems disingenuous because he had the power to commute Mary's sentence at any time if he had felt justice required such clemency. Additionally, when Johnson suspended the writ of habeas corpus in Mary's case -- thereby rendering the writ that Aiken had obtained from Judge Wiley a nullity -- Johnson made it clear that he did not want Mary to escape the hangman's noose.

But Johnson's charge that Holt had withheld the petition from him stuck to Holt; he spent the rest of his life attempting to vindicate himself of the charge.