So this older answer of mine has been linked (thanks /u/EdHistory101 and /u/Randolpho) but I would briefly expand on the text there, as it is highly relevant, but being written for a slightly different question - the offer to Lee of the command of American forces - there are additional points worth adding.
The most important is to emphasize what the underlying implications of this claim is. As the initial, linked post should make clear for anyone who actually clicked through, it isn't wrong to say that Lee joined the traitors because of his Virginian roots, but to do so in that way misses much of the context (and aside from my response, definitely don't miss /u/secessionisillegal's below in the thread, as he drills down deep into the issue). The intention of focusing on this is, essentially, to absolve Lee of any thing that might stain the saintly reputation attached to him in post-war mythology. It both removes the imputation of his being a traitor to his country - "He had no choice! He had to go as Virginia did!" - as well as divorcing him from support for slavery - "He didn't fight for slavery, he fought for his dear Virginia!".
The first, I believe, is dealt with adequately in the afore linked post, even if not dwelled on, namely in focusing on the dichotomy between Lee and Scott, both of whom were Virginians. Many Virginians turned traitor and tossed in their kepis with the Confederacy, but certainly enough stayed loyal to the United States to make clear this was a choice, not an obligation. A few other names of prominent Unionist, Southern officers are present in the thread, including Maj. Anderson and Gen. Thomas, and more broadly, the Southern states provided well over one hundred thousand soldiers for the United States Army, with every rebel state but South Carolina providing at least a regiment of white soldiers. Those numbers included members of Lee's family, his cousin Samuel Phillips Lee serving honorably in the American navy during the conflict, and quite openly contemptuous of those who put state before country.
The second point though is one which isn't covered much in the linked post, and this is Lee and slavery. Many attempt to portray Lee as personally opposed to slavery, and again, that he fought solely for principle of loyalty to state, but the historical record rejects this on multiple counts. The first is that Lee's family benefited massively from slavery, and Lee himself was actually known to have a cruelside in his discipline and punishment of the enslaved persons under his thumb. I touch on this in this longer piece on the concept of the "nice" slave owner, and will quote the paragraph on Lee here:
One infamous example I would use is that of Robert E. Lee. Although the popular image of him is that of the conflicted, but honorable, Southern gentleman who held a personal dislike for slavery, this is a fairly erroneous picture in a number of ways, but he is generally held up as a "nice" slave owner, which again, is an oxymoron. What I would focus on here specifically is his use of punishment though, specifically when to of the people that his family owned tried to escape and gain their freedom but were captured and brought back. He certainly didn't hold back on a whipping for either of them, and he supposedly ordered that the wounds be doused in salt-water afterwards as well for an additional burst of pain. Even if we talk only in comparative terms, and state that as far as slave owners go Lee was hardly the worst of them, that is small consolation to the two men who wanted only freedom, and were cruelly punished in their attempt to gain it.
We can add far more here, noting that these enslaved persons, left in his care by the will of his father-in-law, were supposed to be freed by the terms of the will after a set period of time, something which Lee attempted to fight against, in a desire to eek out every bit of value he could before losing control over the labor of these people. /u/sowser expands on Lee as a slaveowner here for further reading.
More conceptually though, this isn't even about Lee himself, but trying to tie into the Lost Cause ideology which separates slavery from the conflict entirely, the underlying implication that we have built up to being that Lee was an honorable man and opposed to slavery, so he wouldn't have fought for slavery, thus the Confederacy must have been fighting for principle. I have addressed this in many answers previously, talking here about the rhetoric of race and secession, here about claims of Confederate Emancipation, and here about how non-slaveholders viewed the causes, but the sum of it all is very simple, namely that everyone knew exactly what they were fighting for - slavery - and Lee knew it too, and Lee accepted that. He also was complicit in it, as I have written about in this previous answer discussing the kidnapping of free black persons, many of them born free in the North, by Lee's army during the Gettysburg campaign, to drag back south and sell into enslavement, something which Lee was quite certainly aware of.
So anyways, hopefully this fleshes things about a bit more, and helps contextualize not just the facts of the claim, but also what the intention behind them is. Feel free to shoot any follow-up questions you might have my way, of course.
While we wait for an answer to this direct question, we can read the answers to some similar questions about Robert E. Lee that have popped up on this sub:
I think the top answer of the first question may be most relevant to your question, OP
While /u/chadtr5 gives a good answer and /u/Georgy_K_Zhukov offers some excellent context, I'll give a bit of a different perspective than chadtr5. This coincides with what Georgy_K_Zhukov wrote about:
There is no question that loyalty to Virginia is absolutely the justification Lee cited before joining the Confederacy, as well as at the time he joined the Confederacy, and he continued to make the claim after the war was over. However, Lee's claim comes with some considerable caveats.
Robert E. Lee is first known to have expressed this justification in a letter to his son dated January 23, 1861, after five states had already seceded:
"If the Union is dissolved and the Government disrupted, I shall return to my native State and share the miseries of my people, and, save in defense will draw my sword on none."
On April 18, 1861, he had a meeting with Winfield Scott, the Commanding General of the U.S. Army (and, incidentally, a fellow Virginian who stayed loyal to the United States). By all accounts, the meeting seemed to be to warn Lee off of resigning and joining the Confederacy. It would seem, then, there were already suspicions about what Lee intended to do—he had met with Francis Preston Blair four days earlier to talk about his military future, whereupon Lee had been noncommittal. On April 20, 1861, two days after his meeting with Scott, Lee resigned from the U.S. Army. He wrote a resignation letter to Scott in which he stated:
"Save in defense of my native State, I never desire again to draw my sword."
On the same day, he wrote a letter to his sister and another to his brother. The letter to his sister read in part:
"With all my devotion to the Union, and the feeling of loyalty and duty of an American citizen, I have not been able to make up my mind to raise my hand against my relative, my children, my home. I have, therefore, resigned my commission in the Army, and save in defense of my native State (with the sincere hope that my poor services may never be needed) I hope I may never be called upon to draw my sword."
And the relevant section in the letter to his brother:
"I am now a private citizen, and have no other ambition than to remain at home. Save in defense of my native State, I have no desire ever again to draw my sword."
After the war, in 1866, he testified in front of a Congressional subcommittee and said essentially the same thing about his motivations:
"...the act of Virginia, in withdrawing herself from the United States, carried me along as a citizen of Virginia, and that her laws and her acts were binding on me."
However, the timing of some of his words and actions allows for more critical examination of his motivations. This is perhaps best explored in the chapter "Lee Secedes" in the book Lee Considered: General Robert E. Lee and Civil War History by Alan T. Nolan.
According to Nolan, in February 1861, Lee had told fellow soldier Charles Anderson essentially the same thing as he had told the others quoted above, when both of them were in Texas, about to head back East:
"I think it but due to myself to say that I cannot be moved . . . from my own sense of duty. . . . My loyalty to Virginia ought to take precedence over that which is due to the Federal Government. ... If Virginia stands by the old Union, so will I. But, if she secedes (though I do not believe in secession as a constitutional right, nor that there is a sufficient cause for revolution), then I will still follow my native State with my sword, and if need be with my life."
However, the same month, he told another soldier, Captain R.M. Potter:
"I saw General Lee (then Colonel Lee) when he took leave of his friends to depart for Washington [from Texas]...I have seldom seen a more distressed man. He said, 'When I get to Virginia I think the world will have one soldier less. I shall resign and go to planting corn.'"
This statement is more in keeping with what he'd written to his son in January, that he would "draw my sword on none" if a war broke out.
Notably, this was still months before Virginia seceded. They had convened their Secession Convention on February 3, but early news coming out of it was that the state would not secede. In early April, the convention voted against secession, only reversing course after Fort Sumter. North Carolina and Tennessee, also in the Upper South, had held public votes to convene Secession Conventions, and both votes failed.
Nolan also points to a series of letters throughout the Secession Winter, dating at least as early as December 1860, in which Lee expressed views of a South vs. North mentality, in which he was already siding with the South. The January 23, 1861, letter to his son is one of them:
"The South, in my opinion, has been aggrieved by the acts of the North, as you say. I feel the aggression, and am willing to take every proper step for redress. It is the principle I contend for, not individual or private benefit. As an American citizen, I take great pride in my country, her prosperity and institutions, and would defend any State if her rights were invaded...[A] Union that can only be maintained by swords and bayonets, and in which strife and civil war are to take the place of brotherly love and kindness, has no charm for me."
In that last line, Lee makes clear that he believes a Union preserved through war was not a Union he had interest in fighting for.
After the war, in an 1868 letter to Gov. Reverdy Johnson of Maryland, Robert E. Lee wrote of his meeting with Francis Preston Blair, which took place on April 14, 1861. This is the meeting in which Lee was allegedly offered a commanding role in the U.S. Army. According to Lee's own account, he told Blair:
"...stating as candidly and courteously as I could, that, though opposed to secession and deprecating war, I could take no part in an invasion of the Southern States."
Taken together, according to Nolan, it seems that Lee's position evolved a bit in the lead-up to his resignation. Lee already was identifying with the Southern cause, and though earlier on, he expressed some sentiment that he would do whatever Virginia did no matter what—including fighting for the U.S. Army should Virginia join the war on the Union side—by April 1861, he decided he would not take part in any military role against the South, even if his home state of Virginia did. Lee would fight for Virginia if Virginia fought on the side of the Confederates. Had they fought on the side of the Union, it is less clear what he would have done, but there is reason to believe he would have resigned anyway and not fought on either side.
Nolan also notes that Lee's account in several of these communications gives at least one factual inconsistency. In the letter to his sister, to his brother, and to Winfield Scott, he says he has resigned, and plans to remain a private citizen, but qualifies this with the statement "save in defense of my native State". In these April 20 letters, he made it sound like he had no idea what Virginia's decision would be. Yet, the Virginia Secession Convention had ratified secession on April 17, with the news announced publicly the following day. On April 19, it was front page news throughout Virginia. Lee already knew what Virginia was going to do, so his "save in defense" statements were disingenuous. The letters' recipients would have known this at the time.
Further, while acknowledging there is no documentary evidence, Nolan makes the case that Lee was probably already in communication with pro-secession Virginia politicians about a possible role in the Confederate armed forces at the time of his resignation. The rapidity was rather stunning, given the era: Lee resigned on April 20, which was not public; on the same day, he received "a message from the commissioner for Virginia" about coming to Richmond to talk about a military role for the South; on April 21, this invitation was made formally; on April 22, less than 48 hours after having resigned from the U.S. Army, he was in Richmond, accepting the Confederacy's offer of a military commission. Thus, any sort of claim he was making that he intended to remain a private citizen was unlikely to be true at the time he resigned. He knew that wouldn't be the case.
A couple of further criticisms of his stance can be made. In his letter to his sister, he wrote that he could not "raise my hand against my relative, my children, my home". Yet, his sister Anne (Lee) Marshall, and her husband William Louis Marshall, were committed Unionists. Robert E. Lee knew this at the time he wrote the letter. He knew what their reaction would be. In fact, his sister cut off all communication with him after receiving the letter, and they never spoke again (Anne died midway through the war). Lee writes in the letter after giving his justification for resigning: "I know you will blame me, but you must think as kindly as you can, and believe that I have endeavored to do what I thought right." So this claim that he could not raise a hand against a relative was at least suspect, if not outright insincere. For any Virginian at the time, siding militarily with either side was likely to result in taking up arms against relatives who fought for the other side. And this is exactly what happened. Anne's son, Robert's nephew, Louis Henry Marshall enlisted on the Union side, so in a very real way, Robert E. Lee "raised his hand against his relative". He had other Virginia relatives as well who fought on the side of the Union, notably his cousin and childhood playmate Samuel Phillips Lee, a U.S. Naval officer who famously wrote in response to Robert's defection: "When I find the word Virginia in my commission I will join the Confederacy."
(cont'd....)
Understanding another individual's "real" motivations, beliefs, or intentions is really hard. It's often impossible to establish these with confidence even if you have the opportunity to directly question the individual, and it obviously only gets harder as we venture further into the past. That said, the evidence supports the conclusion that Lee fought for the Confederacy primarily because of his loyalty to Virginia.
In August 1866, Montgomery Blair, Lincoln's postmaster-general and the son of Lincoln's advisor Francis Preston Blair wrote in a published letter that his father had offered Lee command of the Union Army on Lincoln's behalf at the start of the war. According to Blair, Lee responded:
Mr. Blair, I look upon secession as anarchy. If I owned the four millions of slaves [of] the South, I would sacrifice them all to the Union: but how can I draw my sword upon Virginia, my native state?
In 1871, the elder Blair gave his account of the conversation:
Lee said that he was devoted to the Union. He said, among other things, that he would do everything in his power to save it, and that if he owned all the negroes in the South, he would be willing to give them up and make the sacrifice of the value of every one of them to save the Union...Lee said he did not know how he could draw his sword upon his native State.
On balance, it seems fair to conclude that Lee made some statement to this effect in 1861. We also have a letter that Lee wrote in January 1861, giving similar views:
The South, in my opinion, has been aggrieved by the acts of the North... As an American citizen, I take great pride in my country, her prosperity and institutions, and would defend any State if her rights were invaded. But I can anticipate no greater calamity for the country than a dissolution of the Union... It would be an accumulation of all the evils we complain of, and I am willing to sacrifice everything but honor for its preservation. I hope, therefore, that all constitutional means will be exhausted before there is a resort to force. Secession is nothing but revolution...
Still, a Union that can only be maintained by swords and bayonets, and in which strife and civil war are to take the place of brotherly love and kindness, has no charm for me. I shall mourn for my country and for the welfare and progress of mankind. If the Union is dissolved, and the Government disrupted, I shall return to my native State and share the miseries of my people, and save in defense will draw my sword on none.
What can we say about that evidence? First, the view that Lee was a "Virginia patriot" is not revisionist. There is clear and direct evidence from Lee's own contemporaneous words. That tends to be one of the strongest types of evidence we can supply for what someone thought or wanted. It's not dispositive, though. Obviously, Lee may have been lying in 1861 -- it's conceivable that he wanted to present a version of his motivations that cast him as especially honorable (on this, it's worth noting that Lee's rhetoric was markedly different than the views expressed by many of his contemporaries which may suggest truthfulness).
Lee's actions at the time tend to support what he was saying. In 1861, Lee was stationed in Texas, which seceded in February. Lee's commanding officer, David Twiggs, surrendered his forces to the Confederacy and immediately took up a commission as a Confederate general. Lee, on the other hand, left rather than join the Confederacy and went to Washington. He accepted a new commission in the Union Army on March 28 (Virginia had not yet seceded).
Lee was in Alexandria, Virginia paying a bill on April 19 when he learned Virginia had seceded. He reportedly remarked in response: "I must say that I am one of those dull creatures that cannot see the good of secession." That night (after midnight thus on April 20), he resigned his commission in the Union Army. Winfield Scott, who then led the Union Army, had been Lee's mentor and Lee wrote to him, "Save in defense of my native state, I never desire again to draw my sword."
He wrote to his sister the same day:
The whole South is in a state of revolution, into which Virginia after a long struggle has been drawn, & though I recognize no necessity for this state of things, & would have forborne & pleaded to the end for redress of grievances, real or supposed, yet in my own person I had to meet the question whether I should take part against my native state. With all my devotion to the Union & the feeling of loyalty & duty of an American citizen, I have not been able to make up my mind to raise my hand against my relatives, my children, my home. I have therefore resigned my Commission in the army, & save in defense of my native State, with the sincere hope that my poor services may never be needed, I hope I may never be called on to draw my sword.
The formulation Lee seems to have favored is a bit self-serving, but let's note that there's not much of an incentive for Lee to lie to his sister about all of this. Overall, the pattern of the evidence for a Virginia-first mentality is very strong. Lee's biographers have tended to view Lee as committed, first and foremost, to Virginia. Douglas Southall Freeman, for example, writes: "He owed allegiance to only two governments, that of Virginia and that of the Union, and there could be no thought of a third so long as these two did not conflict and Virginia did not throw in her destiny with the Confederate States."
I don't know if all of this makes Lee seem like a good person or not (that's for you to decide), but it does seem fair to say that Lee supported the Confederacy because Virginia seceded and his loyalties lay with Virginia. It's not the question you asked, but let's note that this is not the same as saying that Lee was actually an opponent of slavery (he wasn't) or that he was somehow a person of unusually high moral character or whatever.
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Finally, there is a lot to be said on this particular topic. While you're waiting for a more in-depth response, you might find this response from u/Georgy_K_Zhukov to a similar question about Lee interesting.