First, let's analyze the military situation in 1865. The entire freshly reannexed Confederacy is coated in a thin layer of Union troops. The Mississippi River and the east coast of the ex-Confederacy, where slave populations are at their highest by any metric, are being patrolled by the U.S. Navy. In this situation, attempting to continue the fight in favor of slavery is all but a lost cause.

Next, the political situation. The governments, federal and state, of the Confederacy were fully overthrown. First, the eleven states were replaced by six military districts, each under the skeptical eye of a Union general. Once again, it is not looking great for anyone who wants to continue slavery in this system. This was not a long-term plan, though; it was just enough to get legislation through Congress as to how the states would be readmitted to the Union, and what their constitutions and laws would look like. Opinions range from 'Radical Republicans' who believe the South should be treated harshly for their secession, to Democrats and their sympathizers who think all that is necessary is for each state to rewrite its constitution and ratify the Thirteenth Amendment (which prohibits slavery).

The sequence of events which results in the Confederacy reuniting with the Union is known as 'Reconstruction'.

As you probably know. President Abraham Lincoln, who advocates for a decently strict, moderate Reconstruction program (to the extent that he vetoes Radical Republican Reconstruction plans), is shot and killed around this time. He is replaced by his VP, Andrew Johnson, who believes that Reconstruction can be wrapped up by year's end (he enters office in April 1865). The entire Republican Party is skeptical of this idea, but the Radicals in particular. Opposition between Johnson and Congress leads nowhere until 1866, when midterm elections give the Republicans sufficient strength to push a Civil Rights Act into law over Johnson's veto. This is the beginning of the end for Johnson; Congress can now make the decisions, and with the ability to repeatedly override vetoes, Johnson doesn't have a meaningful say in the matter. So the Radical Republicans take over the duty of managing the South. This definitely does not bode well if you would like to keep your slaves in secret.

The troops are not recalled from any part of the Confederacy, partially because they are needed to keep the peace - uprisings in the Reconstruction South are not uncommon, with a massacre in New Orleans taking fifty black lives. It is decided that the South will only accept the black vote as an institution of their society if it’s backed up by a military threat. And indeed, if you know anything about what happens to the black vote after the troops pull out (it’s swallowed up by Jim Crow), this decision was correct.

The election of Ulysses S. Grant would be the final nail in the coffin for any supposed slave-supporting minority. A Republican who sat somewhere between moderate and radical, he was absolutely willing to increase the power of the federal government to intercede in cases where the vote was not being granted to all for whom it was their right. The power of the black vote, combined with the disenfranchisement of the most egregious among Confederate supporters, resulted in Republican-controlled state governments which slowly succeeded the military district system. Now a federal eye was not needed to ensure that the South kept its promises to the Thirteenth, and now additionally the Fourteenth and Fifteenth, Amendments. However, Grant’s prolific use of military force, even as far north as New York City, riled up Democrats who saw themselves as oppressed under a military one-party dictatorship. This would lead to the organization of groups such as the Red Shirts, the White League, and the Ku Klux Klan, supported as a way to harass and even kill black voters in order to reclaim the South for the Democrats. They succeeded, and laws such as poll taxes and grandfather clauses, designed to disenfranchise black voters without the need for armed support, shortly followed.

Reconstruction is an extraordinarily controversial topic. Some applaud the willingness of the Radical Reconstructionists to enforce true freedom and liberty in the South by any means necessary; others say that the way those Republican-fielded amendments and laws were forced upon the South was not very free at all. However, the need for military intervention once again in the enforcement of civil rights legislation in the 1960s has convinced many modern historians that the only way to truly stamp out institutionalized racism is to provide the letter of the law with some significant backup.

I have access to JSTOR through uni, so I apologize if these are inaccessible, I don't think I have a way to tell which articles are free and which aren't on my end. These will make for nice further reading if you're in the mood.

https://www.jstor.org/stable/2197687 - An Analysis of Some Reconstruction Attitudes

https://www.jstor.org/stable/23183396 - Acts of Enforcement: The New York City Election 1870

https://www.jstor.org/stable/2701820 - Reconstruction Revisited