▁the ▁Army ▁of ▁Northern ▁Virginia ▁for ▁the ▁rest ▁of ▁the ▁war . ▁Lee ▁began ▁by ▁driving ▁McC le ll an ▁from ▁the ▁Pen ins ula ▁during ▁the ▁Seven ▁Days ▁Batt les ▁of ▁late ▁June ▁and ▁be ating ▁a ▁Union ▁army ▁a ▁second ▁time ▁near ▁Bull ▁Run ▁in ▁August . ▁ ▁App oint ment ▁to ▁the ▁Western ▁Theater ▁and ▁V icks burg ▁John ston ▁was ▁prem ature ly ▁dis charg ed ▁from ▁hospital ▁on ▁November ▁ 2 4 , ▁ 1 8 6 2 , ▁and ▁appointed ▁to ▁command ▁the ▁Department ▁of ▁the ▁West , ▁the ▁principal ▁command ▁of ▁the ▁Western ▁Theater , ▁which ▁gave ▁him ▁tit ular ▁control ▁of ▁Gen . ▁Bra xt on ▁B rag g ' s ▁Army ▁of ▁Tennessee ▁and ▁L t . ▁Gen . ▁John ▁C . ▁P ember ton ' s ▁Department ▁of ▁Mississippi ▁and ▁East ▁Louisiana . ▁( The ▁other ▁major ▁force ▁in ▁this ▁area ▁was ▁the ▁Trans - Miss iss ippi ▁Department , ▁commanded ▁by ▁L t . ▁Gen . ▁The oph ilus ▁H . ▁Hol mes , ▁station ed ▁princip ally ▁in ▁Ark ansas . ▁John ston ▁argued ▁throughout ▁his ▁ten ure ▁that ▁Hol mes ' s ▁command ▁should ▁be ▁combined ▁with ▁P ember ton ' s ▁under ▁John ston ' s ▁control , ▁or ▁at ▁least ▁to ▁rein force ▁P ember ton ▁with ▁troops ▁from ▁Hol mes ' s ▁command , ▁but ▁he ▁was ▁unable ▁to ▁conv ince ▁the ▁government ▁to ▁take ▁either ▁of ▁these ▁steps .) ▁ ▁The ▁first ▁issue ▁facing ▁John ston