Counter-terrorism and elimination of religious extremism were important parts of Sheikh Hasina’s election manifesto. But the concern about terrorism is not limited to top Awami League leaders and is also felt by a major section of the Bangladesh public. Many supported the Awami League in the hope of reversing the rising trend of extremism and terrorism in the country. In her very first press conference after winning the elections, Sheikh Hasina stated that she will not allow the country's soil to be used by terror groups and proposed a joint task force in the subcontinent to tackle terror.

The mutiny by the troops of Bangladesh Rifles (BDR) on 26 February 26 was extraordinarily brutal. The mutiny toll was about 81 with 72 still missing. Many of these were officers of the Bangladesh army. Three mass graves were discovered. Many bodies were thrown into the sewer pipelines. Many of those killed were stripped, mutilated, bayoneted and shot. The Director General of the BDR, Major General Shakil Ahmed was killed in cold blood. Even his wife was not spared. Her dead body was discovered in one of the mass graves.

India’s position stands vindicated. It had for long maintained that not only have insurgents from the north east found safe havens in Bangladeshi soil but that they have enjoyed the backing of the Bangladeshi state as well. These allegations have now been proven with the confessional statement of Md. Hafizur Rahman and Din Mohammad, the two accused in the Chittagong arms haul case. This was the largest arms haul in Bangladesh, which had taken place on April 2, 2004 in the Chittagong area.