Pemberton was put in his place commanding the Vicksburg, Mississippi garrison. Bowen was assigned to fortify the post of Grand Gulf with a brigade of infantry. Over the next several weeks, he constructed naval batteries along the river. After becoming convinced that Grant would land near Grand Gulf, he repeatedly requested Pemberton for additional supplies and men but each request was refused.
At the Battle of Port Gibson, Bowen, despite being severely outnumbered, managed to delay Ulysses S. Grant's Army of the Tennessee for most of a day and he personally led two counterattacks. For his stand, he was promoted to major general on May 25, 1863, although his nomination was never approved by the Confederate Congress.Despite pleas for reinforcements, Pemberton and General Joseph E. Johnston failed to react quickly and Grant was able to resume his march through Mississippi. After uniting with the rest of Pemberton's army, Bowen was given a division.
 He next fought at the Battle of Champion Hill, where a counterattack by his division almost split Grant's army in half. When the rest of the army failed to support his attack, Bowen was forced to retreat. After battle Pemberton retreated to Vicksburg and he ordered Bowen to cover the retreat.He suffered defeat at the Battle of Big Black River Bridge on the Big Black River. Accompanying Bowen to Mississippi was his wife, Mary Kennerly Bowen of St. She refused to be separated from her husband.
Louis to enter the war, Mary was by his side, leaving their two young children, Menard Kennerly (age 7) and Anna (age 2) at the family home to be cared for by Mary's mother.  He took part in the final defense of Vicksburg, helping in the defeat of Union assaults, but grew ill with dysentery during the siege. Early in the siege, Bowen tried to negotiate surrender with Grant, a friend from the antebellum days, but was turned away; he did help ease the negotiations that led to the July 4 surrender. After being paroled, he succumbed to dysentery and died near Edwards, Mississippi. He was at first buried near where he died in Mississippi but his body was later transferred to the Confederate States Army Cemetery in Vicksburg.
Following his death, he was praised by his contemporaries as being one of the best generals of the Western Theater and referred to by one biographer as being the real "Stonewall of the West". Other contemporaries also believed that Bowen, "was not second to any Major General then in the Confederate Service".  An attempt after to war to erect a monument to Bowen failed to raise the necessary funds.  His bust stands in the Vicksburg National Military Park near Stockade Redan on Graveyard Road with his brigade. The item "Civil War Era CDV Confederate General John Bowen Vicksburg" is in sale since Saturday, October 6, 2018.This item is in the category "Collectibles\Militaria\Civil War (1861-65)\Original Period Items\Photographs". The seller is "civil_war_photos" and is located in Midland, Michigan.
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