Sheridan found the cavalry units in Virginia widely scattered, their camps filthy, the horses broken down, and the men poorly armed. While he straightened out the routines, reestablished discipline, and cleaned up the camps, he became convinced that the Cavalry Corps was being misused carrying messages, escorting infantry officers, patrolling enemy territory, and guarding a perimeter sixty miles in circumference.

Totaling nearly nine hundred printed pages in two volumes, Jones's Diary touches on a kaleidoscope of issues, events, and people. Recounting a purported conversation with Jefferson Davis, Jones claimed that Davis doubted northerners' ability to wage a hard and costly war. Having resided among northerners, Jones wrote, "I know them better. And it will be found that they will learn how to fight and will not be afraid to fight." This entry, among others, could have been added after the war to give an impression of Jones's foresight and analytical ability.

The Civil War broke Thomas physically, mentally, and financially. The erratic behavior and occasional violent outbursts that his contemporaries noted before the war became so serious that in 1867 his wife committed him to the state asylum in Raleigh. For the rest of his life, with short exceptions, Thomas lived in hospitals for the mentally ill. Ironically, from his hospital room Thomas made one final and very significant contribution to his Cherokee people.