Holt was also a fine orator and was able to sway the Democratic Convention to name Richard Johnson as Van Buren's running mate. Despite this, Holt remains what Elizabeth Leonard called "Lincoln's Forgotten Ally." When Lincoln took office, the new president received aid from Holt in keeping Kentucky, a crucial border state, largely in the Union column. Later, Lincoln named him Judge Advocate General, a position which placed him in charge of a vast machine of military discipline. It also got him embroiled in some highly political cases, such as that of Clement Vallandigham.

When Lincoln was shot as part of a conspiracy to kill not only Lincoln but also Vice President Andrew Johnson and Secretary of State William Seward, Holt became chief police officer, prosecutor and assistant to the defense all at once. While several conspirators were found guilty, the convictions of likely co-conspirator John Surratt and Confederate President Jefferson Davis eluded him. Holt's career continued despite his being involved in the Tenure in Office controversy, and he did not resign until after President Ulysses S. Grant took office. When Holt died in 1894, the New York Times noted that he was one of the last living links with the Civil War leadership.

This dissertation provides a synthesis of numerous primary and the few secondary sources pertaining to Holt, putting forth a unique portrait of what might be termed a reluctant Unionist: a man from the border states with slaves himself but with a desire to stay with the Union. America today is different in several ways from what it might have looked like without Joseph Holt.