Rosecrans did not immediately pursue Bragg and "give the finishing blow to the rebellion" as Stanton had urged. He paused to regroup and study the logistically difficult choices of pursuit into the mountainous regions to the west and south of Chattanooga. When he was ready to move, he once again maneuvered in a way to disadvantage Bragg. The Confederates abandoned Chattanooga and withdrew into the mountains of northwestern Georgia. Rosecrans threw aside his previous caution under the assumption that Bragg would continue to retreat and began to pursue with his army over three routes that left his corps commanders dangerously far apart. At the Battle of Davis's Cross Roads on September 11, Bragg came close to ambushing and destroying one of Rosecrans's isolated corps. Realizing the threat at last, Rosecrans issued urgent orders to concentrate his army and the two opponents faced each other across West Chickamauga Creek.
The Battle of Chickamauga began on September 19 with Bragg attacking the not fully concentrated Union army, but he was unable to break through Rosecrans's defensive positions. On the second day of battle, however, disaster befell Rosecrans in the form of his poorly worded order in response to a poorly understood situation. The order was directed to Brig. Gen. Thomas J. Wood, "to close up and support [General Joseph J.] Reynolds's [division]," planning to fill an assumed gap in the line. However, Wood's subsequent movement actually opened up a new, division-sized gap in the line. By coincidence, a massive assault by Lt. Gen. James Longstreet had been planned to strike that very area and the Confederates exploited the gap to full effect, shattering Rosecrans's right flank.
Whether he did or did not know that Thomas still held the field, it was a catastrophe that Rosecrans did not himself ride to Thomas, and send Garfield to Chattanooga. Had he gone to the front in person and shown himself to his men, as at Stone River, he might by his personal presence have plucked victory from disaster, although it is doubtful whether he could have done more than Thomas did. Rosecrans, however, rode to Chattanooga instead.
The Edge of Glory, Rosecrans biographer William M. Lamers
The majority of units on the Union right fell back in disorder toward Chattanooga. Rosecrans, Garfield, and two of the corps commanders, although attempting to rally retreating units, soon joined them in the rush to safety. Rosecrans decided to proceed in haste to Chattanooga in order to organize his returning men and the city defenses. He sent Garfield to Maj. Gen. George H. Thomas with orders to take command of the forces remaining at Chickamauga and withdraw.
The Union army managed to escape complete disaster because of the stout defense organized by Thomas on Horseshoe Ridge, heroism that earned him the nickname "Rock of Chickamauga." The army withdrew that night to fortified positions in Chattanooga. Bragg had not succeeded in his objective to destroy the Army of the Cumberland, but the Battle of Chickamauga was nonetheless the worst Union defeat in the Western Theater. Thomas urged Rosecrans to rejoin the army and lead it, but Rosecrans, physically exhausted and psychologically a beaten man, remained in Chattanooga. President Lincoln attempted to prop up the morale of his general, telegraphing "Be of good cheer. ... We have unabated confidence in you and your soldiers and officers. In the main, you must be the judge as to what is to be done. If I was to suggest, I would say save your army by taking strong positions until Burnside joins you." Privately, Lincoln told John Hay that Rosecrans seemed "confused and stunned like a duck hit on the head."
On the morning of the 21st we took the train for the front, reaching Stevenson Alabama, after dark. Rosecrans was there on his way north. He came into my car and we held a brief interview, in which he described very clearly the situation at Chattanooga, and made some excellent suggestions as to what should be done. My only wonder was that he had not carried them out.
Ulysses S. Grant, Memoirs
Although Rosecrans's men were protected by strong defensive positions, the supply lines into Chattanooga were tenuous and subject to Confederate cavalry raids. Bragg's army occupied the heights surrounding the city and laid siege upon the Union forces. Rosecrans, demoralized by his defeat, proved unable to break the siege without reinforcements. Only hours after the defeat at Chickamauga, Secretary Stanton ordered Maj. Gen. Joseph Hooker to travel to Chattanooga with 15,000 men in two corps from the Army of the Potomac in Virginia. Maj. Gen. Ulysses S. Grant was ordered to send 20,000 men under his chief subordinate Maj. Gen. William T. Sherman, from Vicksburg, Mississippi. On September 29, Stanton ordered Grant to go to Chattanooga himself,as commander of the newly created Military Division of the Mississippi. Grant was given the option of replacing the demoralized Rosecrans with Thomas. Although Grant did not have good personal relations with either general, he selected Thomas to command the Army of the Cumberland. Grant traveled over the treacherous mountain supply line roads and arrived in Chattanooga on October 23. On his journey he encountered Rosecrans in Stevenson, Alabama, and received a briefing on the state of the Chattanooga forces, but gave no hint to Rosecrans that he had made the decision to relieve him. Grant executed a plan originally devised by Rosecrans and Brig. Gen. William F. "Baldy" Smith to open the "Cracker Line" and resupply the army and, in a series of battles for Chattanooga (November 23–25, 1863), routed Bragg's army and sent it retreating into Georgia.