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Thayer's resignation was handed to the Secretary of War at an inopportune time. Cass and his small staff were struggling to handle the dangerous problem of troop assignments in the South during the South Carolina crisis, a step required by the President's public statement that he would use force if necessary to stop the nullification attempt. There were also other problems, including the settlement of pension claims and preparing to submit Indian treaties to Congress. He took no immediate action on Thayer's resignation, merely telling General Gratiot to tell Thayer that it would be acted on at the proper time. That he was surprised and, to a certain degree, shocked is evident, for he also told Gratiot that he could not understand the resignation, which assumed that "an officer possesses the right to decline a service which constitutes an integral part of his legitimate duties." This statement is puzzling because Cass routinely processed requests for reassignment by other officers. Nearly two months passed before Cass informed Gratiot that Thayer's resignation would become effective after the June examinations.
Ten days before he was notified that his resignation was accepted, Thayer was promoted to brevet colonel. The War Department issued other orders affecting the Academy. General Order 48 reduced graduation leave from four to three months, a specification that remained in effect during peacetime for many years. The same order required an officer to serve at least three years with his regiment before being assigned to special duty. This had a direct impact on the Academy because it was customary to assign distinguished graduates as instructors immediately after graduation. This same restriction applied to the War Department staff and other staffs as well, but the West Point faculty interpreted this to be another Jackson attack on the Academy.