In May 1854, six weeks before Morton was due to graduate, the university's Board of Regents dismissed the head of the medical department, Dr. J. Adams Allen, a popular faculty member. That evening, Morton, a friend and admirer of Allen's, addressed a mass meeting protesting Allen's dismissal and other seemingly autocratic actions taken by university officials. On the following day, Morton was expelled from the university, ostensibly for excessive absences and for general inattention to his duties as a student. His expulsion prompted protests from the student body and across the state. He was readmitted after signing a very conditional document, stating that if the charges against him had been true, then his expulsion would have been justified. The readmission did not last: the university's president, Henry Philip Tappan, released a version of his statement from which the conditionals had been removed, making it a straightforward admission of fault; Morton wrote a letter to the "Detroit Free Press" in which he retracted his original statement, declaring that he had not "...meanly petitioned, implored and besought the Faculty for mercy, for... the Latin-scratched integument of a dead sheep". He was re-expelled and not allowed to graduate with his class. In 1856, under unclear circumstances, he was awarded an honorary Bachelor of Arts degree by Union College of Schenectady, New York; in 1858, the University of Michigan faculty reversed his expulsion and awarded him a diploma.