Here's your 10-point cheat sheet to this big story:
Ten people allegedly belonging to right wing organisations were named as the accused in the case. One of them, Sunil Joshi of Madhya Pradesh, a former Rashtriya Swayamsevak Sangh (RSS) member like Aseemanand, was murdered while the case was being investigated.
Besides Swami Aseemanand, Devendra Gupta, Lokesh Sharma, Bharat Mohanlal Rateshwar alias Bharat Bhai and Rajendra Chowdhary faced trial and were cleared. Two other accused are missing.
The police in Hyderabad, the first to investigate the blast, had blamed the Harkatul Jihad Islami group and rounded up around 100 Muslim young men. They were released in 2008. The National Minorities Commission alleged that they had been falsely charged, illegally confined and tortured.
The CBI in 2010 said Hindu right wing group Abhinav Bharat was behind the blast. According to the chargesheet, the accused were "angered by terrorist attacks committed on Hindus and their temples" and wanted to "avenge" them by attacking Muslim areas and places of worship.
Aseemanand was arrested by the CBI in 2010. The chargesheet said he made a confessional statement before a magistrate in Delhi and disclosed the conspiracy behind the bomb blasts in different places, including Mecca Masjid. Aseemanand allegedly retracted the statement later.
The "confession" was among the documents that were reported missing last month from the Tis Hazari court in Delhi.
Last year, Aseemanand was acquitted in the Ajmer Dargah blast case and also got bail in the Samjhauta Express blast case of 2014.
Swami Aseemanand -- whose real name is Naba Kumar Sarkar -- and Bharat Mohanlal Rateshwar are out on bail while three others are in the central prison in Hyderabad.
Reacting to the acquittals today, former Home Ministry officer RVS Mani said, "I had expected it." He claimed that "all the pieces of evidence were engineered" and that "there was no Hindu terror angle".
In 11 years, over 200 witnesses were examined by the court and over 400 documents were exhibited.