Lincoln opposed slavery, but did not think that he (if elected president) had the power (constitutionally) to abolish it. (His election platform was to prevent its spread into new territiories - which he did think he had the constitutional authority to implement).

Both wartime expediency and wartime opportunity led Lincoln to issue the Emancipation Proclamation. He thought it would be useful. He also thought that using his war powers he could emancipate the slaves constitutionally (only in the rebellious states, not in the Union (border) states where slavery was legal).

Lincoln gave the 'reason' for fighting the Civil War, and expressed his views on slavery in his Gettysburg Address:

"Four score and seven years ago our fathers brought forth on this continent, a new nation, conceived in Liberty, and dedicated to the proposition that all men are created equal.

Now we are engaged in a great civil war, testing whether that nation, or any nation so conceived and so dedicated, can long endure."

Source: http://www.abrahamlincolnonline.org/lincoln/speeches/gettysburg.htm

In this great speech, that genius Abraham Lincoln managed to cover, in a few short words, both reasons for fighting the civil war: A democratic nation, 'conceived in liberty" cannot 'long endure' if the minority which is outvoted by the majority can just say, "Well, we didn't like that vote. We secede."

Democracy only works if a majority on a constitutional issue is binding. If it is not, democracy will not 'long endure' and anarchy, or some other form of government will replace it.

The United States was "dedicated to the proposition that all men are created equal". Slavery is a denial of that proposition. Lincoln ran on a platform to ban the further spread of slavery into the territories. He didn't think (if elected) that he had the constitutional authority to ban slavery in states where it already existed, but he clearly thought it was incompatible with the essential tenets of the 'New Nation'.

It was, of course his election, bringing with it the promise of banning the spread of slavery, which caused the secession, threatening the concept of Democratic government.

Lincoln, quite eloquently expressed that the Union was fighting for two reasons, to oppose slavery where possible, and to preserve Constitutional Democracy as a form of government.

The war made the abolition of slavery possible (constitutionally) in the rebellious states (at least according to Lincoln's interpretation) and he took the opportunity and acted with the Emancipation declaration.

The emancipation proclamation applied only to states in rebellion, which did not recognize his authority. It did not apply to states still in the union and slavery persisted in Kentucky and Delaware until passage of the 13th amendment.

Slavery was not outlawed nationwide until the 13th amendment was passed and ratified by the states in 1865. He did sign that, and it passed the house vote only after some savvy political maneuvering on Lincoln's part (the first house vote in 1864 failed).

So...technically, congress freed the slaves, but it took some greasing of the wheels on Lincoln's part to get the amendment passed.