The attacks in Ajmer and Hyderabad took place in 2007. Three people were killed in the Ajmer attack in October; another nine had died in May in the Hyderabad explosion.
Three years later, new evidence suggests that the investigating agencies and the government got it all wrong. The Central Bureau of Investigation (CBI) says it now believes that radical Hindu groups planned those blasts.
What's led to this new theory is the arrests last week of three men by the Rajasthan Anti-Terror Squad. They were tracked down because they were using SIM cards found in the debris after the attack at Ajmer.
The men arrested are all Hindus, and are believed to be associated with Abhinav Bharat, a Hindu radical group that allegedly planned and executed a terror attack in Malegaon in Maharashtra in 2008. Six people were killed, and more than one hundred injured.
Among those arrested for that attack were Sadhvi Pragya Singh Thakur and an army officer, Lieutenant Colonel S P Purohit for the Malegaon attack. Their alleged agenda: to target Muslim crowds.
Purohit, in recent interrogation, has allegedly said that a man named Sunil Joshi was behind the Ajmer blast of 2006. That's what the Rajasthan police also suspects.
Joshi allegedly knew Sadhvi Pragya well. He died in December 2007, but phone records show that he was in touch with one of the three men arrested for the Ajmer blasts last week.
"Colonel Purohit, arrested for Malgaon blast, has confessed that Sunil Joshi had organised the Dargah operation with the help of Devendra Gupta," Rajasthan Home Minister Shanti Dhariwal told The Hindu newspaper on May 2.
The CBI says that in both the Ajmer and Hyderabad blasts, identical explosives were used. Cellphones triggered both bombs.
The initial allegation that Pakistan-based groups were behind the Ajmer and Hyderabad blasts of 2007 meant that young Muslims paid the price. Muslims like Ibrahim Junaid, who, along with 25 others, was picked up from the Old City of Hyderabad and accused of terror links. They were reportedly tortured in illegal custody. There was no chargesheet accusing them of links to the Mecca Masjid attack. Instead they were accused of conspiring to wage war against the state, of preparing and playing out CDs of the Gujarat communal riots of 2002 to create communal tension.
"Without proof, they arrested our children. They didn't even inform us. We didn't know their whereabouts for 7-8 days," said Arifunnisa, Junaid's mother.
All 26 men were later acquitted but they say the stigma never goes away. Junaid says, "When there is a blast, youth of a particular community are targeted. They are playing with our lives. That happened to me. I lost a year in college. I was not able to do my MD because of this.''
Junaid and some of the other Muslims who were arrested have gone to court against their arrests.
"We are demanding compensation from the police officers who tortured us. That they should be made to pay compensation from their salary, says Rayeesuddin.