In April 1865, Confederate General Robert E. Lee was Commanding General, Army of Northern Virginia and General-In-Chief of the Armies. General Lee was not supreme military officer of The Confederate States of America, a position equivalent today being Chairman, Joint Chiefs of Staff. President Jefferson Davis was Commander-In-Chief of ALL Confederate military forces, a supreme military command position Davis never relinquished. More simply put, on April 9, 1865, when Rebel General Lee surrendered the Army of Northern Virginia to Union General Ulysses S. Grant, that tragic and costly American Civil War was not ended. The fighting continued.
The Confederacy had other armies with other general officer commanders. And periodic battles and skirmishes continued between Yankees and Rebels. For example, take a quick look at the engagement in Texas at the Battle of Palmito Ranch, May 12-13, 1865, where more than 125 United States citizens became causalities. See reference: Battle of Palmito Ranch
This date might better express the end of the American Civil War. On June 2, 1865 Confederate General Edmund Kirby Smith, Commander of Confederate Forces west of the Mississippi, signs the surrender agreement offered by Federal negotiators. General Smith’s surrender marks disestablishment of the last recognized Confederate army, thus bringing a formal end to the historical most bloody and destructive four+ years in United States history. Now the enlisted cannon fodder can finally go home. But even then, some minor skirmishes continue where men and animals became casualties of this divided conflict of unspeakable horror. If the American Civil War was ended April 9, 1865 with General Lee's surrender, then why was it necessary in early June 1865 for another surrender agreement by Confederate General Smith?