The Stage II Comprehensive Examination is a diagnostic examination, the purpose of which is to test a student's preparedness to undertake thesis research. The format of this aspect of the comprehensive requirement is that of a public, oral presentation of a thesis proposal, followed by questioning from the student's Stage II Committee and any other members of the university community who may be present. A written thesis proposal is submitted prior to the examination. Normally, the Stage II examination must be completed within seven full terms of enrolling in the PhD program.

The Stage II Comprehensive Examination Committee consists of the supervisor and at least two additional faculty members from the Department. The composition of the Stage II Committee must be approved by the Graduate Committee, and the Associate Chair for Graduate Studies will act as a neutral chair of the committee of examiners, or will appoint a faculty member to serve in that capacity.