Placed in command of the Department of the Pacific in California he resigned as soon as Texas seceded from the Union, although he dutifully waited for his replacement to arrive before leaving his post. President Davis made him a full general, the most senior Confederate officer to hold a field command and was put in charge of the Western Department. He formed the Army of the Mississippi and prepared for the invasion he knew was coming, even though he had more to defend with less troops than any other senior southern officer. In 1862 Union forces captured Fts Henry and Donelson and later the city of Nashville, Tennessee. Although he was not to blame, Johnston accepted responsibility for these losses and bluffed the Union armies while he gathered his forces at Corinth, Mississippi. On April 6, 1862 General Johnston launched a massive surprise attack on General Grant's Union army at Shiloh. Leading from the front with great courage, he was struck in the leg by a bullet while leading an attack against the last Union position still holding out. He had sent his own surgeon to tend the wounded enemy and bled to death before he realized the seriousness of his injury.
Without his leadership, the Confederates lost the battle of Shiloh in a Union counterattack the following day. Jefferson Davis said that his loss was "irrepairable" and ordered national mourning for the fallen Texan. Since that time, historians have debated the question of what would have been different if General Johnston had not bled to death that day at Shiloh Meeting Church. Few would argue that the Union victory in the war was won in the west, not the east where General Lee consistently held off far superior forces throughout the conflict. The western department, however, saw crucial losses for the south, such as Vicksburg, Atlanta and the bloody "March to the Sea" which wrecked the southern infrastructure. Could General Johnston have made a difference in all of this? It is a debateable point, after all, he would have had more to defend with fewer troops and less reliable subordinates. Yet, given how close the Confederates came to victory in spite of these odds, with stalemates in Kentucky, the crushing victory at Chickamauga and the hair-raising fighting in Georgia, from what we know about General Johnston it seems plausible that he could have carried the day for the south.
When one takes stock of what made General Robert E. Lee a success in the east what most often comes to mind is his audacity, aggressiveness and strategic thinking as well as his ability to work well with both his political superiors and his subordinates; he could also inspire intense loyalty among his men. When these traits are listed beside the western department commanders, Sidney Johnston alone fully measures up. General Pierre G.T. Beauregard, his immediate successor, was a bold and talented commander but the antagonism between him and President Davis meant his constant transfer from post to post. General Braxton Bragg had a good pre-war record and was close friends with Jefferson Davis; however, his harsh discipline, while it did toughen the army made him very unpopular with his troops and his subordinate generals were always at the edge of mutiny against him. General Joseph E. Johnston was respected by his comrades, admired by his troops and was an excellent strategist, however, he and Davis despised each other and his natural caution made him unwilling to take big risks. Finally, General John Bell Hood had the necessary traits of boldness and aggressiveness in abundance, was friends with Davis but his rapid promotion caused many of his more senior subordinates to resent him and numerous opportunities for victory were lost.
In General Albert Sidney Johnston, however, the South seemed to have the perfect winning combination. He worked well with his generals, many of whom he had commanded in the 2nd Cavalry, and his personality and powerful appearance made him greatly admired by his men. He also had the audacity to take the initiative and make bold and surprising attacks. He had the full confidence of President Davis, and old and trusted friend and his hard earned reputation from Texas, Mexico and the southwest meant that he was also feared by his northern opponents. In short, he had all of the qualifications to be a commander in the west with the success General Lee had in Virginia. By preventing the loss of key southern cities, or even at a minimum making these far more difficult and costlier to take may well have been enough to break the northern will to fight and won the independence of the Confederacy.