Following the dissapointment of Murfreesboro - where the Confederates seemed on the cusp of a great victory only to end up conceeding the battlefield and retreating to Tullahoma - Braxton Bragg is heavilly criticized by his subordinates for his conduct of the battle. He becomes deeply depressed and dispondent with the lack of support he was recieving from his subordinates and, despite recieving the support from President Jefferson Davis and General Joseph Johnston - then commanding the Department of the West - he decided to step down as the Commander of the Army of Tennessee.
This leaves that Army without a commander. The only logical solution is to give the position to Joe Johnston so he will likely be given the job. So, with this in mind, a number of questions would need answering, split into two sections.
1) what happens when Grant crosses the Mississippi at Bruinsburg? Who does Davis send to help Pemberton if Johnston is busy with the AoT?
2) how does Johnston fair in Tennessee against Rosecrans? Does he do any better in the Tullahoma Campaign than Bragg did? Does the Tullahoma Campaign even happen if Johnston is there?