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Back in Qum, Khomeini remained something of a theological maverick. At the Madresseh Faizieh, he lectured on the need for Islamic mullahs to involve themselves in politics, as the prophet had done. Khomeini also taught a course in ethics that was, in reality, a discussion of political science from an Islamic viewpoint. Despite his unorthodox ways, or perhaps because of them, he became increasingly popular with students.
"As soon as classes were over, the instruction really began," recalls one former student and colleague, Ayatullah Mohammed Javad Bahonar. "The discussions would go on for hours. He was never pleased unless you could stand up to him. He demanded research and curiosity. He wanted you to ask, to probe, to argue. The two issues he emphasized were the necessity for Islam and Iran to be independent of both Eastern and Western colonialism and the need to get the clergy put of the mold of an academic straitjacket. He said the clergy had a responsibility for humanity not only in Iran but wherever people were hungry and oppressed. In this way Khomeini trained 1,200 religious leaders who are the elite of the country today."
Says Professor Mehdi Haeri, one of his students from this period: "Every weekend, when there were no classes, he used to have a large open class for anyone who wanted to come. He discussed ethics and morals, describing very complicated subjects simply. His secret was that he convinced you he was teaching from the bottom of his heart. You felt the immanence of God; God was ever present with Khomeini."
During the late 1930s, the religious community in Qum came under heavy pressure from the Reza Shah, who had undertaken a campaign to modernize his country, in the manner of Turkey's Mustafa Kemal Atatürk. By 1941, as a result, the number of students at the Faizieh had dropped from several thousand to 500. Khomeini urged the new director of the school, the Ayatullah Boroujerdi, to oppose the Shah more openly. When Boroujerdi refused, Khomeini was bitterly disappointed. Thereafter he called on his superior only once a year, as required. Shortly after Reza Shah was deposed by the British and the Soviets in 1941, Khomeini published a polemic attacking the Pahlavi dynasty for its efforts to bring down the clergy. In 1944, he acquired further recognition by being the only cleric who refused to rise when the new Shah came to visit the school.
When Dr. Mohammad Mossadegh came to power as Iran's Premier in 1951, Khomeini welcomed his anticolonialism and his opposition to the Shah, though he considered Mossadegh too secular. Khomeini had much more sympathy for the Ayatullah Abolqasem Kashani, who was then Mossadegh's partner. Kashani later split with him and may even have cooperated with the CIA-backed coup that toppled Mossadegh's government in August 1953 and enabled the Shah to return to his throne. Khomeini still identifies himself with Kashani, whose memory is reviled by Iranian nationalists because of his alleged betrayal of Mossadegh. One link between Kashani and Khomeini is the Fedayan Islam, a group of fanatical Muslim nationalists who opposed the secular government.