The Anti-Terrorism Squad (ATS) which initially investigated the case and the Central Bureau of Investigation (CBI) to which the case was later handed over to, had argued that the arrested belong to the banned Islamic outfit Students' Islamic Movement of India (SIMI).

The line of investigation changed only after the arrest of Swami Aseemanand who confessed that it was the right-wing Hindu fundamentalists who masterminded the Malegaon blast. Apart from this, many other terror attacks in the country including the Samjhauta Express bombings, Mecca Masjid bombing and the Ajmer Sharif Dargah blast are said to be the work of Hindu extremists.

Upon suspicion of the involvement of right-wing groups behind these attacks, the National Investigating Agency took over the cases of Mecca Masjid, Ajmer Sharif and Malegaon blasts.

The relieved young men and their families were thankful to two people in particular, the slain ATS chief Hemant Karkare and advocate Shahid Azmi. It was this brave anti-terror officer, Karkare, who brought into light the involvement of the right-wing extremist behind the terror attacks by arresting Colonel Prasad Purohit, Sadhvi Pragya Singh Thakur, and the self-proclaimed Shankaracharya Dayanand Pandey alias Sudhakar Dwivedi.  Karkare was killed during the 26/11 Mumbai attack in 2008. The young advocate Shahid Azmi refused term these young Indians as anti-nations and fought for the accused until he was shot dead in 2010.

The families of victims as well as the wrongly accused have decided to put more pressure on the government to bring the real culprits to book. They also demanded the youth be given adequate compensation and call for a genuine investigation against the officers who framed them. However, the damage to their credibility, the fears and the sufferings the families undergone cannot be repaid and when they ask, “We want our dignity and five years back,” the faulty investigative agencies and the government are left with no answers.