While Bangladesh's deceased former Prime Minister Khaleda Zia and her party, the BNP, always adopted an anti-India policy, things took a turn for the worse in India during her stints as the Bangladesh Prime Minister from 1991 to 1996 and 2001 to 2006. It was during this period that armed separatist organisations of the North East, like the ULFA, NDFB, NLFT, ATTF, had become very strong in North-East India.
Though credited with restoring democracy after a period of tumultuous military rule in the country, Zia’s BNP is said to have been sheltering the leaders of militant groups in the North East.
The intensity of terror attacks in the North East has always been dependent on how conducive the environment in their neighbourhood has been, and during the BNP rule, the attacks were mostly successful. For instance, Assamese groups such as the United Liberation Front of Asom (ULFA) and the National Democratic Front of Bodoland (NDFB) thrived during the 1990s and early 2000s during Zia’s rule. India alleged that the BNP government connived with Pakistani agencies to extend support to armed north east Indian insurgent groups and that the top leadership of these groups were encouraged to live in peace and comfort in Bangladeshi cities.
From 2001–06, there was also a rise of Islamic militancy and terror outfits are said to have maintained connections with various BNP leaders like Tarek Zia and Lutfozzaman Babar. It is also known that a lot of weapons and explosives were entering North-East India from Bangladesh at that time. Allegations were rife that 10 trucks of arms were shipped through Bangladesh to insurgents in the North–east under the direction of top officials of the BNP regime in 2004.
Interestingly, around the same time, the coalition government of Bangladesh (BNP and Jamat-e-Islami) was focused on the country's internal security, political tensions, and combating terrorism, launching anti-militancy operations like 'Operation Clean Heart'.
Despite this, they continued harbouring anti-India separatist organisations in India. The lack of diplomatic dialogue between India and Bangladesh and the lack of cooperation between border surveillance and security during the BNP rule contributed to this.
However, the situation changed dramatically when the rival Awami League (AL), led by Sheikh Hasina, swept to power in the 2008 general elections. Hasina adopted a "zero tolerance" policy towards Indian insurgent groups, leading to a significant crackdown. They not only shut down anti-India insurgent camps but also extradited several top insurgent leaders to India.