Prior to his return to Pakistan in 1976, the secretive development program on nuclear deterrence was near completion and Hoodbhoy was aware of the program. Hoodbhoy maintains his close ties with Pakistan's vibrant nuclear society, and had collaborated with many of country's leading theoretical physicists throughout his career, mainly with Ishfaq Ahmad. On several occasions, Hoodbhoy staunchly countered Dr. Abdul Qadeer Khan's "father-of" claims, and roundly criticized his academic research on nuclear physics. In the 1980s, he famously debated with Bashiruddin Mahmood on the topics of sunspots, life-after-death, and philosophy.