Interesting hypothetical. I agree with others that Lincoln had little choice but to replace McClellan when he did or shortly thereafter. They just disagreed too strongly on how to carry out the war.
Having said that, had McClellan somehow remained in command, the war would most definitely have taken a different course. The Battle of Fredericksburg would most definitely not have occurred, at least not in the manner in which it unfolded. After that, all bets are off on where the war might have gone. Presumably, McClellan would have continued his slow pursuit of Lee into Virginia and maybe even still tried to force the Rappahannock at Fredericksburg. I suspect, given his background and (few) strengths, McClellan would have made sure the pontoons were there when he needed them, but I can't imagine he would have decisively attacked even if he HAD stolen a march on Lee. I suspect he would have stalled until Lee was there in force and then pulled back across the river and went into winter quarters without giving battle.
By spring, he would have been under massive pressure to advance so he would have again tried to force the line of the Rappahannock, perhaps upstream as Hooker did or downstream somewhere, perhaps even with the help of the Union navy to drop him at some point along the York/James Peninsula to have another go at attacking Richmond from the east. Again though, it is simply impossible to see how McClellan could have accomplished any possible plan without Lee reacting more quickly and putting himself on strong ground between McClellan and Richmond. That would put McClellan immediately on the defensive, and open him up to a counterstroke by Lee. I suspect that, by midsummer 1863, the situation would again see Lee on the offensive and the Union army trying to counter. That is not to say such an offensive would end up in Pennsylvania again, but it would have resulted in Lee marching north and at least approaching the Potomac.
For all his timidity on the offensive, McClellan knew how to retreat and keep his army intact and fight a defensive campaign (as an example, he was a fool to have let Lee gain the initiative like he did during the Peninsula Campaign in 1862, but, once Lee took the offensive, McClellan was fairly masterful in keeping his army intact as it retreated). As such, I don't see a Chancellorsville happening under McClellan. He would have seen to his flanks and, while he undoubtedly would have been driven back... either in battle or by maneuver... I highly doubt the AOP or any piece of it would have been broken even briefly. Rather than a rapid advance north by Lee, it would have been a slow one with McClellan doing a reasonable job of countering Lee's maneuvers and keeping from either a decisive battle or a from making a quick dash deep into the north.
I should add that I think 1863 was a bit of a watershed for Lee. Early in spring, he had a health crisis. At the time, it was called "rheumatic fever", but, based on the symptoms, it sure sounds like he had a heart attack. Now, you've got a man who has an entire "nation" depending on him who is most definitely feeling his mortality and likely greatly weakened. As such, he likely saw the 1863 campaigning season as perhaps his last and only chance to win the war. I am convinced that THIS is why Lee took such long chances at Chancellorsville and Gettysburg. He felt like his army was as strong as it would ever get and he had the Union army in front of him and might not live to get another clean shot at them with anything close to even odds. This also means that, no matter who was in command of the Union army and no matter what the tactical situation, Lee would have made an all out attack during the summer of 1863 throwing every soldier he had into one (what he hoped would be a) climactic battle. With McClellan in charge, I expect it would have happened somewhere in Northern Virginia rather than further north, perhaps at a Third Battle of Manassas. Here is the key. A third Battle of Manassas would have happened in "friendly" territory. Lee would have had access to local spies and had people on his staff with thorough knowledge of the terrain and, hopefully, Jeb Stuart would remain close rather than going off on a snipe hunt. All of this might just have given Lee the advantage, even if it was a set piece battle with the two sides slugging it out like they did at Gettysburg.
Even so, the only way this changes the war is if McClellan's army is destroyed on the battlefield. If it is able to retreat back toward Washington, the strategic situation remains the same and I don't see McClellan letting his army get destroyed. In the end, a great battle is fought and it is a Confederate victory, but it is not a great enough victory to change the course of the war. Maybe Lee raids into the north while McClellan licks his wounds behind the Washington defenses, but Lee probably shot his bolt in the great battle and would, thus, be unable to sustain his army for long in the north. They would get fat and happy during the harvest and pull back into Virginia before the leaves fall and before McClellan could get behind them.
Now what? I would say that Grant is still brought east in early 1864 and promoted above everybody else to take command of all Union armies just as he was without McClellan in the picture. Almost certainly, McClellan would take this as an affront and resign in March 1864 (perhaps still to run for president a few months later). Or perhaps his egomaniacal desire to be a hero on the battlefield would outweigh his other egomaniacal desires and he would stay on under Grant. Regardless, with Grant on the scene, Grant becomes the de facto commander of the Army of the Potomac and McClellan becomes little more than a clerk who passes orders from Grant to his corps commanders and the remainder of the Civil War proceeds much like it actually did with a massive and bloodly overland campaign that eventually results in the fall of Richmond and the surrender of Lee.
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