Major Willis F. Jones left Kentucky in the fall fo 1861 to cast his lot with the Cofnederacy, leaving behind a wife anbd small children. He became a major/AAIG and was named as the adjutant for his cousin, MGEN Charles W. Field, when Field was appointed to command Hood's old division in the I Corps of the Army of Northern Virginia, then in East Tennessee, the fighting efficiency of which had been severely compromised by the actions of Micah Jenkins and James Longstreet. Field restored the fighting efficiency of the unit by his positive leadership, and the divison once again became one of Lee's most dependable units.

Jones was mortally wounded while delivering orders at Second Darbytown (Charles City Road) on October 13, one of only a handful of Confederate casualties on that day when Butler's attempt to turn the Confederate left was foiled.

The Rev. William Norwood, of St. John's Episcopal Church, Richmond conducted funeral services for Jones on October 15, 1864, with interment in Hollywood Cemetery. The information on his funeral is contained in J. Staunton Moore, ed., The Annals and History of Henrico Parish, Diocese of Virginia, and St. John's P. E. Church. Rev ed., Baltimore: Genealogical Publishing Co, 1979 (Originally published in Richmond, 1904), at p. 360.

A handful of Jones' letters to his mother and wife, sent across the lines by the parole and exchange boat, are found in the Jones Family Papers, Filson Historical Sopciety, Louisville.