Why did Lincoln go to war against the confederacy during the civil war?

Slavery

http://en.wikipedia.org/wiki/Us_civil_war#Causes_of_the_war

No, as the Union determined that secession was illegal, and thus did not recognize the Confederate States of America, there was no Declaration of War. This Civil War was fought, by the Federal States, strictly to preserve the Union... emancipation of the slaves was more of a punitive, tactical result of the war. President Lincoln, while personally opposed to slavery, was not an abolitionist.