On retiring to Rossville, he found himself, in the absence of Rosecrans, McCook, and Crittenden at Chattanooga, the senior officer in that part of the field, and he immediately began the work of reorganizing the troops of the several divisions gathered indiscriminately there. He succeeded in reorganizing a large number of men, and, selecting a strong position at Rossville Gap, endeavored to open communication with General Thomas. This was found impracticable, however. During the night General Thomas retired to this position, and, forming a junction with General Negley, ordered him to post the forces along the line selected by him, and prepared to give the enemy a warm reception on the next morning. Bragg was too wise to attack, and contented himself with merely reconnoitering the position. On the succeeding day the troops were retired to Chattanooga, and preparations were made for the siege which followed. During this siege General Negley was relieved from duty by General Rosecrans in such a manner and so unjustly that he was induced to demand an examination into his official conduct. This was granted; a court of inquiry was convened and an investigation made, resulting in General Negley's acquittal. The official record of the court states in conclusion "that General Negley exhibited throughout the day (the second day of the battle) and the following night great activity and zeal in the discharge of his duties, and the court do not find in the evidence before them any ground for censure." General Negley, on the conclusion of the trial, was ordered to report to the Adjutant General at Washington, and did so, but soon after resigned. He is now engaged in the cultivation of his farm near Pittsburg, Pennsylvania.