When Johnston arrived in Jackson he had a grand total of 6,000 men to call upon. Upon taking command of the position he learnt from John Gregg and W.H.T. Walker of the Confederate defeat at Raymond and that Sherman's Corps was between him and Pemberton. "I am too late" he said in a message to Richmond, with the force immediately at his disposal little more than a division and the Federals at Clinton preventing an easy link up with Pemberton he could do little of immediate value. 9,000 reinforcements were on the way but they might not, and indeed did not, arrive in time to prepare properly for a defense of Jackson let alone an attempt to break through to Pemberton.
Walker and Gregg had told him that Sherman was isolated at Clinton. With this in mind Johnston sent orders to Permberton to march on Clinton with as strong a force as he thought practicable, attack Sherman and break through to join up with him at Jackson. Pemberton answered that he would move immediately with 16,000 men but did not. He slept on his orders, decided they were wrong and convince the senior officers of his army in a council of war that they would be better off marching south to strike at Grant's supply lines.
In the mean time Johnston discovered just how wrong Gregg and Walker had been.
Sherman wasn't isolated at Clinton. McPherson's corps was close by in support. Not only was McPherson operating in close support with Sherman but Grant was with them and they were marching on Jackson. Johnston's reinforcement from further east had not yet arrived, he could not guarentee that they would arrive in time nor in what state they would be in when they arrived to be of much use to any attempted defense of the city, and the two corps advancing upon him had a numerical advantage well over two to one. Johnston thus saw a potential defense of Jackson to be detrimental to his army and the campaign and instead decided to gamble on losing the city but linking up with Pemberton for only union with Pemberton would permit the Confederates to face the Federals on an even footing.
Johnston only learnt after he's began to march up the Canton road that Pemberton had not obeyed his orders and was marching south instead of east. He sent further orders to Pemberton, reaffirming his original order and stating that he would move to join him. This time Pemberton obeyed.
Unfortunately one of the men Johnston trusted to get his orders to Pemberton turned traitor and took those orders directly to General McPherson who sent them on to General Grant who acted with his usual decisiveness to move to prevent any attempt to link up. What followed was Champion Hill.
Pemberton, defeated, fell back to Vicksburg. Johnston, learning of Pemberton's defeat, counciled him to march north, leave Vicksburg to the defense of the Militia and join up with him so that they could face the Federals on a more or less even footing and defeat them in oper battle. Pemberton ignored this council, fell back into the cities defenses and sent a message to Johnston saying he awaited further orders.
Johnston was now the only major Confederate force out in the open in Mississippi. His reinforcements had arrived and with Loring's division - the only one to escape being trapped in Vicksburg - he had approximately 20,000 men. Grant, investing Vicksburg, quickly swelled his numbers until they reached approximately 77,000 men. By the time Johnston had built an army the size of the one Pemberton took with him into Vicksburg it was already too late.
Pemberton turned Johnston into an almosy mythical saviour during the siege of Vicksburg, using his name to rally the people in their conviction to withstand the seige. He knew, however, that Johnston had no intention fo lifting the siege but instead was insisting that any attack against the Federal would only be with the eventual goal of breaking the Army of Mississippi out, that Johnston thought Vicksburg was doomed and would not waste his mens lives trying to save it regardless of the political circumstance surrounding its fall. Pemberton, for his part, refused to give up on Vicksburg and kept sending pleas for Johnston to ride to the rescue of the city, refusing to understand the military reality of the situation.