Pemberton and Johnston should have combined and used the tactical advantage of defense to make Grant's army pay dearly for every inch of ground between the Pemberton-Johnston Army and Vicksburg.
Why was Joseph Johnson's army in Jackson, Mississippi instead of combining with Pemberton?
The real problem is that Pemberton had received contradictory orders. President Davis told Pemberton to hold onto Vicksburg and not abandon it. Johnston told Pemberton to abandon Vicksburg and keep his army intact. Pemberton chose to follow Davis' orders and proceded to get himself trapped in Vicksburg.
This plan to unify Pemberton and Johnston still has problems as Grant began the campaign with 44,000 men and would later be reinforced by 30,000 additional men. Johnston and Pemberton combined only had about 36,000 men so they would need reinforcements or a lucky break that let them engage only part of Grant's army. Johnston's force received about 25,000 reinforcements although many probably did not arrive before Grant's reinforcements in early June. Still, it would be a race against time for Johnston to assemble enough troops to outnumber Grant before Grant was reinforced. There were about 10,000 Confederates in Arkansas and Louisiana, but the Union controlled the river. Crossing over to Mississippi would have been difficult.
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