The North was fighting to preserve the Union. The Southern states seceded because of slavery (another way of articulating this is because they were interested in preserving states' rights to decide the slavery issue).

Ta-Nehisi Coates' recent article is a great and timely analysis of the origins and legacy of the CSA

The basic issue dividing the North and the South from the time of the Missouri Compromise until Fort Sumter was the political unbalance to national politics that the perpetuation of slavery in the South caused. Most Northern states had black slaves at the time of the revolutionary war but all those states ended their slavery. After the Missouri Compromise, which divided the states into slave and free, much of the political debate centered on trying to maintain a political balance between the slave states and the free states. In the North, abolitionists pushed for ending all slavery on humanitarian grounds, an idealistic movement which arose along side movements to limit alcohol consumption and create communal living. These movements all had roots in a Protestant revival thinking. In the South, Radicals such as John C Calhoun began to defend slavery as a positive good. It is important to understand these were the extremes on both sides. However, Northern Republican leaders in the 1850s did want to end the expansion of slavery into the new territories won in the Mexican War and the South wanted slavery to expand freely. When Stephen Douglas proposed the new states should be allowed to vote on their slave/free status, virtual war erupted in Kansas. Lincoln clearly did not think well of slavery; however, he in no way wanted to end the practice. He did however want to limit slavery's territory. This was unacceptable to Southerners, who seceded. Since a democracy cannot survive if the losers in an election do not accept the result and since America was at the time the only real democracy in the world, the north felt it had to fight to preserve the Union or democracy would fail as a political system. The North did not begin the war to end slavery; it fought because the South refused to accept the political decision (as reflected in the election of 1860) that the political power of the slave states would be curtailed. Lincoln tried to compromise to keep slave states in the Union--this is reflected in the fact that border states such as Maryland, Delaware and Kentucky (and technically poor Missouri was a border state too)--were allowed to maintain slavery and that technically their state of slavery was not even affected by the Emancipation Proclamation. However, even slave states with relatively few slaves, such as Virginia, seceded and war was inevitable. Neither side anticipated how truly hellish the war would be; in fact, in the Battle of the First Bull Run spectators went out to watch the fun. The clearest way to think of the situation is that only a small group of abolitionist radicals wanted to emancipate the slaves in 1860 but that after the pressure of an extremely violent war a majority of Northerners wanted to end slavery. (Although a current and quite viable historical perspective is the slaves basically emancipated themselves by escaping to freedom as the Union army approached.) However, Northern republicans did want to diminish the political power of Southern slave politicians--largely by ending the expansion of slavery into new territories and by opposing conquering Caribbean nations to create new slave states--and the South seceded because it refused to accept the political decision of 1860. Thus the Civil War did begin ultimately over slavery.