Thomas to Halleck: "I have made my last protest while the war lasts. You may hereafter put a stick over me if you choose to do so. I will take care, however, to so manage my command, whatever it may be, as not to be involved in the mistakes of the stick."
After the defeat of the Union army at Chickamauga, which was saved from being a complete rout only by the improbable stand of Thomas against Bragg's entire army (25,000 against 60,000), Rosecrans fortified Chattanooga, abandoning the heights of Lookout Mountain and Missionary Ridge to Bragg. Rosecrans was thus safe for the moment, but his supply situation was critical and got worse.
For various reasons (chaos also in the Confederate supply situation, horrendous losses at Chickamauga, strong fortifications around Chattanooga) Bragg decided to starve Rosecrans out rather than attack whereby it wasn't exactly clear, who was besieging whom. Bragg was also occupied with trying to clean out all of the insubordinate elements in his army who had contributed greatly to limit his options before the battle. One of the most insubordinate elements was Longstreet, the savior from the East. He had expected Davis to name him Bragg's replacement, and he jumped feet first into the rebellion among Bragg's officers, aligning himself against Bragg, of course. But Davis came to Chickamauga, listened, saw, and stuck with Bragg.
Bragg tried to placate Longstreet by giving him the responsibility for the entire left flank (Chattanooga Valley, Lookout Mountain, Lookout Valley, and beyond), but Longstreet was not to be mollified. He displayed complete indifference to his charge, disobeyed Bragg's order to throw back Hazen (who had effected the crossing at Brown's Ferry on 27 Oct.), and disobeyed Bragg's order to use "all necessary force" to oppose Hooker who had entered Lookout Valley from the West on 28 Oct. Instead, Longstreet ordered an improvised night attack by a division against Hooker's rear guard - a division at Wauhatchie under Geary. This accomplished nothing, and Hooker was there to stay as long as he wanted. This stabilized the line of supply from the Nashville railroad to Stevenson, Ala., from there via steamboat to Kelley's Ferry, and on to Chattanooga via the easy wagon route past Raccoon Mountain to Brown's Ferry - the "cracker line". Having thrown away Bragg's entire left flank, Longstreet then lobbied with Davis in order to be sent back to Virginia, stopping on the way to try and chase Burnside out of Knoxville.* Davis so ordered, and Bragg concurred, wanting to be rid of Longstreet anyway, and hoping the threat to Burnside would draw away some of Grant's forces from Chattanooga.
For Grant had arrived on 23 Oct. On 19 Oct. Thomas had taken over the command of the Army of the Cumberland from Rosecrans who had not recovered from the debacle at Chickamauga. Thomas began immediately reorganizing the army and solving the supply problem (following a plan worked out by Baldy Smith and Rosecrans). Grant approved of the plan which was already underway. Meanwhile Grant was preparing his own plan which was designed to make Sherman the victor (and himself the architect thereof) of the coming battle against Bragg. At this time Sherman was slowly approaching Chattanooga from western Tennessee with Grant's former army, the Army of the Tennessee, now Sherman's (Grant had been promoted to Cmdr. of the Division of the Mississippi).
However, Thomas and Grant didn't like each other very much. Grant felt uncertain of himself in Thomas's presence, seeing in him the only possible rival for overall command. On the other hand, Thomas didn't like Grant's improvised way of doing battle. Moreover, Thomas didn't really need Grant's help to deal with Bragg. For a complete summary of this situation see my article "Politics in the Union Army at the Battle for Chattanooga". Grant's hidden or not so hidden agenda (promote Sherman, get himself called East to take on Lee, open other paths to success after the war) was therefore in conflict with that of Thomas who merely wanted to decisively defeat Bragg and shorten the war.
In a nutshell, Sherman arrived late and performed incredibly badly in his task of taking the northern end of Missionary Ridge. This series of lapses allowed Thomas to shift his effort to where he wanted to make it in the beginning, namely against Bragg's southern flank at Rossville Gap. According to Grant's plan, Hooker was to be held in reserve, and maybe demonstrate a little bit, and Thomas was only to demonstrate and then join Sherman in his victory march down the ridge. Sherman's delay enabled Thomas to get "permission" for Hooker to attack Lookout Mountain on 24 Nov. while Sherman was crossing from the north bank of the Tennessee opposite the northern and practically undefended end of Missionary Ridge. Hooker took Lookout Mountain. Sherman's botched reconnaissance (resulting in his stopping far short of his objective in his orders - the railroad tunnel - on the afternoon of 24 Nov.) allowed Thomas to get orders for Hooker to attack Rossville Gap.
The afternoon of 25 Oct., while Sherman was being defeated piecemeal by Cleburne (who had less than a quarter of the forces that Sherman had), Hooker took Rossville Gap and sent troops in 3 columns north toward Bragg's headquarters on Missionary Ridge. Osterhaus (Sherman's division stranded on the south side of the Tennessee by a break in a pontoon bridge and then borrowed by Hooker), even got around far to the rear of Bragg's position and probably started the panic in Southern ranks which then helped Thomas's troops to break the Bragg's center in 6 places during the famous charge up the ridge. Maybe it started even earlier as they watched Hooker with 12,000 men or so cross the valley unopposed toward their left flank and their road back home if he so chose.
This charge began as Grant's order for a limited demonstration in order to draw away pressure from Sherman. Thomas's troops were supposed to advance to the foot of the ridge "take the rifle pits" and stop - a really bad order because the soldiers would have been directly exposed to defending fire from above. In various ways, Thomas stalled the execution of this order until he knew that Hooker was around behind Bragg. When the troops did take the rifle pits, they continued the charge up to the crest (4 to 500 feet above the flats, inclination up to 45%), and broke through. There is dispute among historians concerning whether this charge was spontaneous, whether the various division and brigade commanders were simply confused, or whether Thomas had in some way ordered the movement beyond the rifle pits behind Grant's back. August Willich, one of the first brigade commanders to reach the top wrote in his report that the order he had been given was to take the crest. Who gave this order?
Grant didn't. Grant's reaction to the charge up the ridge, described as being everything from mild surprise to cursing and rage, proves with certainty that he had not ordered the charge and decidedly did not want it. Grant had proven already, and would prove again many times later, that he was not particularly motivated by a desire to keep as many of his men alive as possible in battle. The main reason for his displeasure, aside from his habitual reaction to any perceived infraction of his orders, was the fear that the charge might succeed. That not Sherman , but Thomas would win the battle (and get the credit).
Afterward, Grant, Sherman, and Halleck did the next best thing and rewrote the history of the battle, making Sherman's failure into a successful holding operation, turning Thomas's charge into a miracle (i.e. one-time fluke), and negating almost altogether Hooker's turning of Bragg's left flank. For a couple of hours Hooker simply disappeared into some sort of black hole in Rossville according to Grant's report.
After the battle, Thomas's Army of the Cumberland was incorporated into Sherman's Army of the Tennessee, and Sherman was put in charge of the drive toward Atlanta (see the Hundred Days campaign). It didn't hurt him that his brother was US senator from Ohio, nor that his father-in-law was a former senator.
* Burnside did a good job at Knoxville, paid Longstreet back for Fredericksburg.