After leaving the Jesuits in 1991, Cassidy earned a Licentiate of Sacred Theology (STL) degree ("summa cum laude") from Saint Paul University and taught ethics part-time for the university. He moved to Toronto to become Director of Research at a small non-government organisation, the Latin American Working Group (LAWG), where he edited "Central America Update", a monthly journal/newsletter providing news and analysis on Central America. Cassidy obtained a conjoint PhD degree in Social Ethics from the University of Ottawa and Saint Paul University, where his thesis on the Ethics of Bernard Lonergan was awarded the University of Ottawa Graduate School's Gold Medal ("Prix de l’École"). He was also awarded a DTh degree by St Paul University.