Human rights agencies were reporting a worrying systemic rot even in the pre-9/11 era. In 2000–01, the army alone registered 120 complaints of alleged excesses by its personnel in Kashmir and the Northeast, the National Human Rights Commission (NHRC) noted in its annual report. Other than the Border Security Force (BSF), no other paramilitary force bothered to even reply to its queries regarding complaints of atrocities. NHRC received at least fiftytwo complaints of human rights violations from the Northeast in 2000–01.

In Kashmir, a team of army and police officers staged a fake encounter to kill five innocents, and claimed they were terrorists. Such brutal acts were not limited to militancy-hit areas. In 1999–2000, NHRC reported 1,093 cases of custodial deaths. The same account said almost every second state reported police brutality, irrespective of the party in power. These trends sharpened after the Kandahar hijack of IC-814 in 1999.

When the ban on SIMI came, less than 1 per cent of Muslims made up the ranks of the Maharashtra state police, far below India’s embarrassingly low 4 per cent Muslim representation in the Indian Police Service (IPS).

The story was not very different in other states: in Uttar Pradesh, just 2.3 per cent of sub-inspectors are Muslims, and a little over 3 per cent head constables and just over 4 per cent constables are Muslims, an RTI query revealed in 2014. The HighLevel Committee on Social, Economic and Educational Status of the Muslim Community of India, headed by Justice Rajinder Sachar, found that just over 3 per cent of the paramilitary force was Muslim. Only 3 per cent of the Indian Administrative Service was Muslim.

With a history of communal riots and the general lack of trust between Muslims and the police in Maharashtra, reliable active intelligence was non-existent from within the Muslim communities.