Why wasn't Robert E Lee prosecuted and executed?

[eppur_se_muova]

16. The paperwork was misplaced, and rediscovered about that time.

Johnson, a Southern sympathizer, was accused of accepting payment for pardons of Confederates -- that's why he was impeached. I find it a little doubtful that he would have refused to pardon Lee -- unless maybe Lee refused to pony up. That might explain the cavalier way in which the document was handled.

President Johnson's amnesty pardons
graphic: Oath of amnesty submitted by Lee in 1865

On May 29, 1865, President Andrew Johnson issued a Proclamation of Amnesty and Pardon to persons who had participated in the rebellion against the United States. There were fourteen excepted classes, though, and members of those classes had to make special application to the president. Lee sent an application to Grant and wrote to President Johnson on June 13, 1865:

Being excluded from the provisions of amnesty & pardon contained in the proclamation of the 29th Ulto; I hereby apply for the benefits, & full restoration of all rights & privileges extended to those included in its terms. I graduated at the Mil. Academy at West Point in June 1829. Resigned from the U.S. Army April '61. Was a General in the Confederate Army, & included in the surrender of the Army of N. Virginia 9 April '65.[145]

On October 2, 1865, the same day that Lee was inaugurated as president of Washington College, he signed his Amnesty Oath, thereby complying fully with the provision of Johnson's proclamation. Lee was not pardoned, nor was his citizenship restored.[145]

Three years later, on December 25, 1868, Johnson proclaimed a second amnesty which removed previous exceptions, such as the one that affected Lee.[146]

https://en.wikipedia.org/wiki/Robert_E._Lee#President_Johnson's_amnesty_pardons
***
In 1865, after the war, Lee was paroled and signed an oath of allegiance, asking to have his citizenship of the United States restored. However, his application was not processed by Secretary of State William Seward, and as a result Lee did not receive a pardon and his citizenship was not restored.[171][172] On January 30, 1975, Senate Joint Resolution 23, "A joint resolution to restore posthumously full rights of citizenship to General R. E. Lee" was introduced into the Senate by Senator Harry F. Byrd Jr. (I-VA), the result of a five-year campaign to accomplish this. Proponents portrayed the lack of pardon as a mere clerical error. The resolution, which enacted Public Law 94–67, was passed, and the bill was signed by President Gerald Ford on August 5.[173][174][175]

https://en.wikipedia.org/wiki/Robert_E._Lee#Legacy

On May 29, 1865, President Andrew Johnson issued a Proclamation of Amnesty and Pardon to persons who had participated in the rebellion against the United States. There were fourteen excepted classes, though, and members of those classes had to make special application to the President.

Lee sent an application to Grant and wrote to President Johnson on June 13, 1865:

"Being excluded from the provisions of amnesty & pardon contained in the proclamation of the 29th Ulto; I hereby apply for the benefits, & full restoration of all rights & privileges extended to those included in its terms. I graduated at the Mil. Academy at West Point in June 1829. Resigned from the U.S. Army April '61. Was a General in the Confederate Army, & included in the surrender of the Army of N. Va. 9 April '65."

On October 2, 1865, the same day that Lee was inaugurated as president of Washington College in Lexington, Virginia, he signed his Amnesty Oath, thereby complying fully with the provision of Johnson's proclamation. But Lee was not pardoned, nor was his citizenship restored. And the fact that he had submitted an amnesty oath at all was soon lost to history.More than a hundred years later, in 1970, an archivist at the National Archives discovered Lee's Amnesty Oath among State Department records (reported in Prologue, Winter 1970). Apparently Secretary of State William H. Seward had given Lee's application to a friend as a souvenir, and the State Department had pigeonholed the oath.



https://www.archives.gov/publications/prologue/2005/spring/piece-lee

The differences between the two sources are interesting.

At the time, I read a newspaper article which claimed Lee's Oath document had been found behind a filing cabinet after more than a century. Apparently, this is something of an urban myth, or a story concocted to cover up negligence or malfeasance.