The following narrative comes from Douglas Freeman Southall's R.E. Lee. Southall's volumes are invaluable to the Lee literature and, in fact, serves as the seminal and definitive work on Lee's life. I have a problem with the volumes though. Southall puts his opinion in Lee's voice, therefore making it appear as if Lee is voicing these concerns, ideas, etc. Unfortunately, these opinions have worked their way into the current Civil War historiography as Lee's opinion and, therefore, as fact. As discerning historians, scholars, or even enthusiasts, it is our responsibility to separate the author's opinion from fact.
"One of Jackson's chaplains, Reverend B. T. Lacy, came to headquarters during the morning of the 7th on his way to find Doctor S. B. Morrison, Early's chief surgeon, whom Doctor McGuire desired in consultation. Jackson was worse, Mr. Lacy said. He had done very well on the 6th except for slight nausea, but at dawn Doctor McGuire had found unmistakable symptoms of pneumonia. There was fear, for the first time, that his illness might be fatal. Lee would not admit the possibility of such an outcome. His own faith in God was so complete that he did not believe Heaven would deprive the South of a man whose services were essential to victory. He said to Lacy: "Give [Jackson] my affectionate regards, and tell him to make haste and get well, and come back to me as soon as he can. He has lost his left arm, but I have lost my right."
What would become of the army if Jackson died? Where, among all his lieutenants, could Lee look for another man to execute with swift certainty the flank marches he so much employed in his strategy? Longstreet was a fine fighter, once the issue was drawn, but Longstreet was slow and contentious, always arguing for his own plan, even to the last minute, whereas Jackson, after advancing his own proposals, would execute Lee's orders as readily as if they were his own. In the Army of Northern Virginia, he had no peer. For him to die would be in very truth for Lee to lose his "right arm."
That evening Jackson was reported better. The pneumonia did not seem to be filling the lung. But the next morning, Friday, May 8, as Lee went about the routine duties of the day, gloom settled again. Jackson was weaker, the pneumonia was advancing, he was in mild delirium at intervals, babbling orders and, with his old concern for the welfare of his men, repeatedly calling, "Tell Major Hawks to send forward provisions for the troops." Despite these ominous symptoms, Lee would not give him up. Jackson could not die, he kept telling himself! He was unable to go to Jackson, both because he could not trust his emotions and because there was no one in whose hands he would feel safe in leaving the army. He had even been compelled to ask the President to come to headquarters for the discussion of important military questions, inasmuch as he felt that his own presence there was essential. There was one thing, only one, that he could do for Jackson. That was to pray for him. On Saturday night, as the doctors shook their heads and expressed the fear that the outlook was hopeless, Lee went down spiritually to the brook Jabbok and, like Jacob, wrestled with the angel. Never in his life had he prayed with so much agony of spirit. While the army slept and Jackson in his stupor fought his battles over, Lee on his knees implored Heaven to grant to his country the mercy of the deliverance of Jackson from death.
When the troops began to gather for worship during the forenoon of the next day — a beautiful Sabbath that the commanding general had recommended as a day of thanksgiving for the victory — Lee was still unconvinced that Jackson would be taken. Eagerly he met the chaplain who came from Guiney's at Jackson's request to preach at headquarters. The face of the clergyman told his story: The doctors ahead given Jackson up and did not believe he could survive, except by a miracle. He was in virtual coma, breathing very badly, and muttering still of his warring. "A. P. Hill," he was saying, "prepare for action." And again: "I must find out whether there is high ground between Chancellorsville and the river . . . push up the columns, hasten the columns. . . ." Even in the face of this, Lee refused to believe it could happen. "Surely, General Jackson must recover," he said, in a shaken voice. "God will not take him from us, now that we need him so much. Surely he will be spared to us, in answer to the many prayers which are offered for him!"
The minister preached to a large company of officers and to a multitude of men who had escaped the fangs of death in the Wilderness, but it is doubtful if Lee heard much that the earnest and eloquent Mr. Lacy had to say. His mind was at Guiney's, with Jackson, and so were his prayers. When the service was over, Lee spoke again to the chaplain: "When you return, I trust you will find him better. When a suitable occasion offers, give him my love, and tell him that I wrestled in prayer for him last night, as I never prayed, I believe, for myself." And he had to turn abruptly away to conceal his emotion."
But it was not to be so. At 3:15, on a beautiful spring day, Jackson’s delirium stopped. With a smile, he said, “Let us cross over the river and rest under the shade of the trees.” And then he closed his eyes, and died.