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Secession and Civil War
Sunday morning, January 20, 1861, the national secession crisis rocked the Yale campus when students and professors awoke to find a secession flag flying above Alumni Hall on the Old Campus. During the night, southern students had broken into the building and raised the flag up the flagpole. It had a large white background with a red cross in the center that spanned the flag's length and width. Depicted in the upper left-hand corner was the cresent moon and palmetto tree associated with the state of South Carolina. Northern students stormed the building but they found the locks plugged up with nails and the doorknobs removed. After failing to break open the doors, they found a back entrance which they used to climb to the roof. Once on the roof, they tore down the flag and took back Alumni Hall. This event made national headlines when the following issue of Frank Leslie's Illustrated Weekly reported the confrontation and illustrated the chaos with three of on-the-scene sketches. Unlike the majority of Ivy League schools during the secession crisis, Yale did not expel its southern students at the outbreak of the war, though the war itself would draw many men back home.

The Civil War began in 1861, and would not loosen its grip until 600,000 Americans -- 166 Yale men -- were dead. The issues fueling the backroom squabbles of a student organization were brought out into the open and decided on the battlefield. Of those killed, 55 were Confederate, 48 from Yale College, and seven from the Yale Law School. The casualty rates for Union and Confederate students were vastly different: 69 percent of Confederates while only 13 percent of the Union alumni, were killed. In 1915, the names of both Union and Confederate dead were immortalized in the freshly cut marble of the Woolsey Rotunda. Yale students' important contributions to the Confederacy, however, came not on the battlefield but within the government.

The Confederacy's Attorney General Judah P. Benjamin (B.A. 1828) later appointed Secretary of War, was the highest-ranking Yale man on either side of the Civil War. He had been expelled before graduating for reasons still contested today. The official records say that he was expelled for "cheating" but there is no further elaboration on the charge. He was at the top of his class and there are no signs that he cheated on his academic work. It has been assumed that he was cheating at cards or engaged in some other form of gambling on campus. Yale men also held power within the private sphere of the Confederacy. Burton N. Harrison (B.A. 1859) was Jefferson Davis's private secretary; Richard Taylor (B.A. 1845) was Davis's son-in-law and President Zachary Taylor's son.

It would be easy to conclude that the return of southern alumni to Yale and the voyages of new southern students would be strained by the events of the early 1860's, but the divisions did not settle as deeply as at many of the other Ivy League schools. With Harvard's proximity to Boston, the seat of abolition, and Brown's expulsion of its southern students during the war, Yale was left in a better position to restore post-war ties with the South. Only Princeton fared better, with its Presbyterian tradition and long-standing complacence toward slavery. Alumni from the South returned to Yale as early as 1866, and by the mid-seventies, ivy from Robert E. Lee's house was planted on the Old Campus during Commencement to symbolize the reconciliation of the Confederacy with the rest of the nation. The Civil War had changed the nation, and each regions concept of itself, but Yale's ability to attract students and scholars was not permanently diminished by the war. With the arrival of the twentieth century, the South would help transform Yale into a great research university.