The Iron Guard was ultimately toppled in the civil war of January 1941, producing the more lenient fascist dictatorship of Ion Antonescu. In June of that year, Popa was co-opted by the authorities to participate in reeducating Guardist sympathizers. With Gala Galaction, Cicerone Theodorescu and Iuliu Scriban, he lectured students at the Iași Costachi Seminary about the excesses of Guardist dogma. He continued to speak his mind, in particular objecting to Romania's participation in World War II alongside Nazi Germany. He was, as Boia notes, "an intransigent antifascist, [who] would naturally fit into any sort of plot against the regime". In 1942, following Rainer's retirement, he was transferred to Bucharest, where he worked as a professor for four years. After Rainer's death in 1944, he also took over the Anthropological Institute and reattached it to the medical school. While there, Popa wrote a study showing the lack of any scientific basis for Aryanism and asserting that there was no reason to oppress Jews. Traian Săvulescu, afraid to offend Antonescu, refused to publish it; Popa nevertheless read the work before the Academy in late 1943. The listeners, few of whom were pro-German, reacted positively. However, a January 1944 address was seen as a veiled attack on the dictator, to whom the members were largely sympathetic, and as a result drew a chillier reaction. One of his conferences at the Academy, "Reforma Spiritului. Știința ca bază de primenire a omului" ("Spiritual Reform. Science as a Basis for Bettering Mankind") objected to Romania's economic dependency, claiming that Romanians were at risk of falling back among "agricultural peoples", those "destined to perpetual ignorance". By that time, the security service, "Siguranța Statului", was keeping Popa under constant surveillance.