While, as a Thomas supporter, I absolutely love the question, the immediate answer is "We Need a Timeline" - the butterflies from this one are too big to give any real answer without one.
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Thomas accepts the position of Chief of Ordinance of the Virginia Provisional Army. When it is integrated into the Confederate armed forces, Thomas receives the rank of Brigadier General and is given command of a mixed brigade in the Army of the Potomac, Beauregard commanding.
Thomas drills his brigade rigorously, but fairly, and his men look up to him. He soon strikes a friendship with fellow Brigadier James Longstreet, who shares many of his views on the military and life in general. Their two brigades, with Bonham's in close support and Early's in reserve, are tasked with guarding the major crossings of Bull Run.
On July 18th, their position is attacked by Tyler's Union division. Posted in a naturally strong position, Longstreet and Thomas fight the northerners off without great difficultly. Morale rises in the ranks.
On July 21st, the Battle of Bull Run is won on the far left flank by Jackson and others. Longstreet and Thomas remained in their positions along Bull Run as ordered.
In the reorganization of the army that follows after the battle, Longstreet is promoted to Major General and given command of a division that contains Thomas' brigade. Their relative rankings are in response to the popular notion that Virginian's are overly represented in command position. Everyone acknowledges that Thomas will be promoted at the first opportunity. In the meanwhile, Thomas serves ably and happily as Longstreet's effective second-in-command.
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OR:
Thomas accepts the position of Chief of Ordinance of the Virginia Provisional Army. When it is integrated into the Confederate armed forces, Thomas receives the rank of Brigadier General and is given command of a mixed brigade in the Army of the Potomac, Beauregard commanding.
Thomas drills his brigade rigorously, but fairly, and his men look up to him. He soon strikes a friendship with fellow Brigadier James Longstreet, who shares many of his views on the military and life in general. Their two brigades, with Bonham's in close support and Early's in reserve, are tasked with guarding the major crossings of Bull Run.
On July 18th, their position is attacked by Tyler's Union division. Posted in a naturally strong position, Longstreet and Thomas fight the northerners off without great difficultly. Morale rises in the ranks.
On the morning of July 21st, when Beauregard and newly-arrived Johnston are informed that their left flank is turned, they immediately send reinforcements from the right of their army in the form of Jackson's brigade. The fighting of the 18th revealed to their satisfaction that only 1 brigade is necessary to hold the main Bull Run crossings. Thomas' brigade is pulled out of line and told to be in readiness to march to the left flank. He is ordered to do so early in the afternoon.
By around 3 o'clock the fighting on and around Henry House Hill is reaching its climax. Jackson's brigade has held off every attack the Union launched against it, but they are tiring. And while the Union troops are becoming increasingly disorganized and losing artillery batteries at an alarming rate, they still hold a formidable numerical advantage if they can be coordinated.
Thomas arrives some distance from Jackson's left fank. He can see that what Union artillery remains in action is posted on a height paralleling Henry House Hill called Chinn Ridge. Furthermore, a regiment of infantry is posted in support, while four more (Howard's brigade) are marching in that direction. A strong Union attack from that prominance would outflank Jackson's brigade. On the other hand, from his own position, Thomas would be on *their* flank.
As he had received no detailed orders one way or the other, Thomas marched his men towards Chinn Ridge. Due to the lay of the land and everyone's attention being focused on Henry House Hill, Thomas' approach is largely undetected. Howard's brigade, one of the last organized Yankee units on the field, is routed. Thomas prudently halts his own attack as the northerners retreat past the Warrenton Turnpike, as his own men have become equally disorganized in victory.
In the reorganization of the army that follows after the battle, Thomas is promoted to Major General and given command of a division. While "Stonewall" Jackson is the great savior of the Confederacy on this day, July 21st, Thomas is recognized as the man who led the attack that ultimately routed the Union army. He serves alongside fellow division commander James Longstreet with the main army, and both men are recognized as highly competent generals.
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OR:
Thomas accepts the position of Chief of Ordinance of the Virginia Provisional Army. When it is integrated into the Confederate armed forces, Thomas receives the rank of Brigadier General and is given command of a Virginia brigade in the Army of the Shenandoah, Johnston commanding.
In the fighting around Falling Waters and Opequon Creek, early in July, the lion's share of the fighting is directed by brigade commanders George Thomas and Thomas Jackson, commanding fellow brigades of Virginians. Facing the very cautious Union commander Patterson and largely green brigade commanders, the fighting goes entirely the Confederates' way. By the middle of the month, Patterson is in full retreat towards Harper's Ferry and will eventually pull back all the way into Maryland.
Soon enough Johnston is called upon to come to the aid of Beauregard at Manassas Junction. He is fixated on the idea of using the railroad as a means of transportation. Jackson's brigade entrains first, followed by Thomas', and then Barnard's. These three arrive in time to fight at Bull Run. Bee's arrives on the field at the very end of the battle.
Jackson's brigade, arriving first, is slated to join the ultimately-aborted attack from the Confederate right flank. Thomas' and Barnard's brigades are held in general reserve. When word comes that the Confederate left flank is turned, these two brigades are immediately sent to shore it up.
Thomas and Barnard make a determined stand on high ground north of Henry House Hill, and delay the Union advance for over an hour. However, they are becoming increasingly outnumbered. Thomas advises Barnard that they must retire on their artillery, then unlimbering on Henry House Hill, and to pull back *now* while they can still do so with order. Barnard agrees, but before they can carry the movement out, a musketball hits Thomas in the left leg. Seriously wounded, he is carried from the field.
Barnard takes the men back to Henry House Hill with very little order, but fortunately for the South that day, Thomas Jackson's fresh brigade is just then arriving to take over the defense. After a hard fight all afternoon, the Union army retires from the field in complete disorder, and Jackson has earned the nickname "Stonewall".
Thomas' leg is amputated at a field hospital back at Manassas Junction. For gallantry on the field he is promoted to Major General. However, it will be 1862 before he is ready to assume active command duties again.
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OR:
Thomas accepts the position of Chief of Ordinance of the Virginia Provisional Army. When it is integrated into the Confederate armed forces, Thomas receives the rank of Brigadier General and is given command of a Virginia brigade in the Army of the Shenandoah, Johnston commanding.
In the fighting around Falling Waters and Opequon Creek, early in July, the lion's share of the fighting is directed by brigade commanders George Thomas and Thomas Jackson, commanding fellow brigades of Virginians. Facing the very cautious Union commander Patterson and largely green brigade commanders, the fighting goes entirely the Confederates' way. By the middle of the month, Patterson is in full retreat towards Harper's Ferry and will eventually pull back all the way into Maryland.
Soon enough Johnston is called upon to come to the aid of Beauregard at Manassas Junction. He is fixated on the idea of using the railroad as a means of transportation. Thomas, however, suggests that in the time it will take for their one train to make multiple two-way trips to Manassas Junction, a single brigade can travel by foot, and volunteers his own men. Johnston agrees.
Thomas arrives on July 20th, and is added to the battle plan as close support for the brigade of Jackson, scheduled to make an attack from the Confederate right the following day. This plan is disrupted, however, when Union infantry is sighted outflanking the Confederate right. The brigades of Barnard and Bee, the general reserve, are sent to stop the Union advance. They slow it down, but by noon are in retreat towards Henry House Hill. The brigades of Jackson and Thomas are immediately sent to stabilize the situation.
Jackson and Thomas, both former artillerists, recognize the natural strength of the Henry House Hill position. They situate their men accordingly, Jackson on the left and Thomas on the right. This position is a natural rallying point for Confederate troops all over the field.
The Union advance continues by mid-afternoon, never coordinated, but with the numerical advantage. Jackson and Thomas hold firm at first, but eventually their men begin to waver. A Union relief column sent to retrieve some captured batteries begins to sneak its way around Jackson's left flank.
Jackson rides to the threatened flank and begins to sort matters out. Locally he is not outnumbered, but the men are tired. Just as it seems like he has matters well in hand, a musketball strikes his right shoulder. Losing blood fast, stretcher-bearers make to carry him from the field, and his men seem about ready to retreat after him.
Jackson forces himself to a sitting position and addresses his troops. "You are Virginians. You shall not retreat from this ground. Look," he says, gesturing to the right, "there stands Thomas like a stone wall. You will hold just as surely as he will." Sure enough, Thomas' brigade is holding the line with no major difficulties.
Re-emboldened, Jackson's men redouble their defense. Thomas, recognizing their plight, takes a regiment from his own line to shore up the left flank. Never once do his or Jackson's men break. By day's end, the Union army is routed and in full retreat to the Washington defenses.
Confederate hero George "Stonewall" Thomas is promoted to Major General and given command of all troops in the Shenandoah Valley. At first it is organized into a division, consisting in part of his old and Jackson's old brigade. The two formations are inseperable in battle after that day, and collectively known as the Stonewall Brigades.
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I can see any of these 4 ideas playing out, or any dozens more. And it seems to me to be mildly futile (at best) speculating any farther than that without at least establishing a TL such as the above four on which to work with.