The blast that that took place on a train going to Lahore from Delhi, killed at least 68 people and left scores injured. However, Aseemanand later claimed he was coerced into confessing. However, he later said the confession had been "coerced out" of him.
Eight of them, including Naba Kumar Sarkar (alias Swami Aseemanand), were chargesheeted. All the accused were related to a radical Hindu group, Abhinav Bharat, which allegedly has close ties with the Rashtriya Swayamsevak Sangh (RSS), an ideological wing of the ruling Bharatiya Janata Party.
BJP's Subramanian Swamy, meanwhile, read a larger design.
Responding to questions on the Hindu terror angle to the case, he said that those were cooked up by the government of the time for political gain.
He also said that witnesses in the case were turning hostile after June 2014 and accused the investigation officer was unable to give a "proper statement".
Investigation against another two, Tejram Parmar and Amit Chowhan, is still on. Swami Aseemanand was acquitted in that case.
The original NIA chargesheet had included ten people for conspiracy and in carrying out the attack with an IED device on May 18, 2007.
Malegaon blasts in 2006: On September 8, at least four blasts outside a mosque in Maharashtra's Nashik district had killed over 38 people. Some of them later alleged torture in custody.
April 7, 2011: NIA takes over the case. During the CBI probe, the role of Hindutva activists came to light.
The case has seen several twists and turns.
March 30, 2017: Aseemanand released from Chanchaljuga jail.
Joshi was shot dead in 2007.
The court stated that the accused were acquitted on account of there being "no direct evidence" against them. "In no other country could this be done, but it was done here", he told ANI news agency.