Five Pakistani generals orchestrated the genocide: President Yahya Khan, General Tikka Khan, Chief of staff General Pirzada, security chief General Umar Khan, and intelligence chief General Akbar Khan. The U.S. government, long supportive of military rule in Pakistan, supplied some $3.8 million in military equipment to the dictatorship after the onset of the genocide.

Yahya appointed the ruthless Lt. General. Tikka Khan, later known as the Butcher of Bengal, as the Governor and GOC of East Pakistan. Pakistan secretly began reinforcing its army in the eastern wing via Sri Lanka.Senior Pakistani officers who are unwilling to cooperate with this nefarious plan such as Lt. General Yakub Khan, GOC East Pakistan, and Governor of East Pakistan, Vice Admiral Syed Mohammad Ahsan, were relieved of their duties.

It was recognized from the first that a campaign of genocide would be necessary to eradicate the threat: “Kill three million of them,” said President Yahya Khan at the February conference, “and the rest will eat out of our hands.” (Robert Payne, Massacre [1972], p. 50.)

On March 25 the genocide was launched. The university in Dacca (Dhaka) was attacked and students exterminated in their hundreds. Death squads roamed the streets of Dacca, killing some 7,000 people in a single night. Places like Chittagong lost half of its population. Destitutes wandered across the country hoping to escape the West Pakistani militia and its forces. Ten million refugees fled to India. The massacres continued for months in East Pakistan.

Younger men and boys became regular targets as they were suspected to being potential freedom fighters. Search operations went on for young men who were not to be seen again.In Death By Government, p. 329. Rummel describes a chilling gendercide ritual, reminiscent of Nazi procedure towards Jewish males: “In what became province-wide acts of genocide, Hindus were sought out and killed on the spot. As a matter of course, soldiers would check males for the obligated circumcision among Muslims. If circumcised, they might live; if not, sure death.”

“They were not the small casual killings of young officers who wanted to demonstrate their efficiency, but organized massacres conducted by sophisticated staff officers, who knew exactly what they were doing. Muslim soldiers, sent out to kill Muslim peasants, went about their work mechanically and efficiently, until killing defenseless people became a habit like smoking cigarettes or drinking wine. … Not since Hitler invaded Russia had there been so vast a massacre.” (Payne, Massacre, p. 29.)

In conducting the killings, there was a priority list. They had identified five sections of the populace as their main enemies:
1) leaders, activists and supporters of Awami League,
2) communists and socialists,
3) freedom fighters and their associates,
4) the Hindu community irrespective of sex or age and
5) students, intellectuals and professionals. Numerous barbaric methods were used to loot, rape, murder, paralyze, torture, humiliate and traumatize these sections of the society although there were atrocities inflicted on civilians not belonging to the resistance as well.

The accounts of horrific tales from the genocide include villages being seized, people organised into group and shot on the spot, Hindus (considered as heretics) taken to slaughter houses and killed and open fire on the public. Teachers from Dhaka University and Rajshahi University were killed. Journalists, physicians, educationists, artists, professionals were also among the ones killed or tortured.