Rai said he too initially believed that the blast, which ripped through the only train between India and Pakistan, was the handiwork of a Pakistani terror outfit aided by the banned Students Islamic Movement of India (SIMI).
However, detailed study of the explosive used by the perpetrators of the crime showed the material was not similar to those used by the terror groups like Lashker-e-Taiba or SIMI. Further probe led them to Hindu right wing suspects.
"The sad part is that the kind of support we wanted from the local police was missing and this took us a little time in solving the entire mystery behind the case," he said.
"As we were zeroing on Sunil Joshi, we received a news that he has been murdered by two of his close associates -- Ram Chandra Kalsangra and Sandeep Dange (both are named as RSS workers by the NIA in its charge sheet in the 2008 Malegaon blast case)," he said, adding his assassination was an attempt to cover up the case.
"The signatures were the same in Malegaon 2008 and Mecca Masjid blast. I had detailed talks with the slain Maharashtra ATS Chief Hemant Karkare which corroborated many things of our case.
"Like we benefited by recovering a suitcase with an unexploded explosive device, Karkare was benefited by recovering the motorcycle (that was used in Malegaon blast). Investigations in both the cases hinted towards Joshi and his team," he said.