Sadr himself was placed under house arrest, which the regime tried to extract concessions from him. During his interrogation of Sadr in August 1979, Fadil al-Barak, the head of the security agency, demanded that he make a public statement denouncing the Iranian Revolution and supporting the Iraqi policy toward Iran. When Sadr refused the regime softened its language, and a new mediator, Shaykh Isa al-Khaqani, was sent to ask Sadr to fulfil only one of five conditions to spare his life: withdraw his support of Ayatullah Khomeini and of the Iranian regime; or issue a statement supporting one of the government's policies such as the nationalization of foreign oil companies and national autonomy for the Kurds; or issue a fatwa forbidding association with the Da'wa party; or revoke the fatwa that prohibited joining the Ba'th party; or be interviewed by an Iraqi or other Arab newspaper that was affiliated with the Iraqi regime. By then Sadr, according to his personal secretary al-Nu'mani, had concluded that his days were numbered any way, and he decided to reject all government demands in anticipation of his martyrdom. He told al-Khaqani, the Ba'th regime's mediator:
"The only thing I have sought in my life is to make the establishment of an Islamic government on earth possible. Since it has been formed in Iran under the leadership of Imam [Khomeini] it makes no difference to me whether I am alive or dead because the dream I wanted to attain and the hope I wanted to achieve have come true, thanks to God."
When the Islamic fundamentalist groups, the Da'wa party and Islamic Action Organization headed by al-Shirazi and the Mudarisi brothers,
saw the regime harassing their leader, they took up arms against the Ba'th officials. They attacked the Ba'th party ideologue Tariq Aziz (then the foreign minister) in Mustansiriyya University. Aziz was supposed to deliver a speech to the Ba'th party members among the university's student body stating the regime's policy towards Iran. Muslim activists threw a bomb at Aziz, injuring him and killing his bodyguards. At the public funeral for the guards another bomb was thrown at the funeral procession, killing several people.
The regime faced for the first time resistance that was undermining its support among the Shi'a. Saddam Hussein, by then the new president of the republic, during a hospital visit to those who has been injured at Mustansiriyya, called for revenge against the perpetrators. The regime's old tactic of labelling the Muslim armed struggle as the work of Iranian elements in the country was no longer convincing because, Muslim anti-government activities continued to flourish even after more than 130,000 Iraqis of Iranian origin had been deported to Iran. Moreover, Sadr, the symbol of the Islamic movement, belonged to a well-known Iraqi family. What the Ba'th regime needed was to liquidate the Islamic movement altogether. On March 31, 1980, the Revolutionary Command Council passed a law sentencing all past and present members of the Da'wa party or its affiliated organizations, or people working for its goals, to death. That law eliminated any possibility of sparing Sadr's life.
Sadr had in any case left no room for retreat. While he was under house arrest, he smuggled three messages to his associates calling on the Iraqi people to resist the regime in any way possible.
In these messages, he spoke as their leader in their name, and he demanded from the government political and religious rights for all people, Shi'as and Sunnis, Arab and Kurds. He even appealed to the members of the Ba'th party, whose leader he accused of violating the principles of the party itself. He challenged the Ba'th leadership to allow the people for only one week to express their hostility to the regime. In one of these messages, Sadr issued an ultimatum: topple the regime and establish an Islamic government in its place:
"It is incumbent on every Muslim in Iraq and every Iraqi outside Iraq to do whatever he can, even if it cost him his life, to keep the jihad and struggle to remove this niare from the land of beloved Iraq, to liberate themselves from this inhuman gang, and to establish a righteous, unique, and honourable rule based on Islam".
The security forces came for Sadr and his sister on April 5, 1980, and detained them in the headquarters of the National Security Agency in Baghdad. Three days later, his body was brought back to his uncle Muhammad Sadiq al-Sadr in Najaf for secret burial. The whereabouts of Bint al-Huda, his sister, were never disclosed by the regime, but it is widely believed that she too was executed.
Two weeks later, Ayatullah Khomeini announced the execution of Sadr and his sister and called on the Iraqi people and the armed forces to overthrow the Ba'th regime.