Here is a 10-point low-down on the case against him:
Lt Col Purohit is accused of floating Abhinav Bharat, collecting huge funds to procure arms and explosives and also organising meetings where the Malegaon attack was planned.
Appearing for Lt Col Purohit in the Supreme Court, senior lawyer Harish Salve argued that the Army officer had been in jail for the past nine years but charges had still not been framed against him.
The investigation was initially conducted by the Maharashtra Anti-Terrorism Squad led by its chief Hemant Karkare. Mr Karkare was killed in the terror attacks in Mumbai on November 26, 2008. The probe was then handed over to the National Investigation Agency (NIA) in 2011.
Since his arrest, Lt Col Purohit has maintained that he was assigned by military intelligence to infiltrate various terror organisations and that his superiors were constantly in the loop about his actions and associations with Abhinav Bharat.
The NIA maintained that there was evidence in the form of audio and video recordings, call data records and the statements of the witnesses which prove his involvement in the case.
The NIA recommended prosecuting Lt Col Purohit for conspiracy and under the Unlawful Activities (Prevention) Act, though it had dropped charges under the stringent anti-terror law, the Maharashtra Control of Organised Crime Act or MCOCA, against him and nine others.
While rejecting his petition earlier, the Bombay High Court had referred to the report filed by the NIA, and said, "Purohit was the one who prepared a separate 'Constitution' for 'Hindu Rashtra' with a separate saffron colour flag. He also discussed about taking revenge for the (alleged) atrocities committed by the Muslims on Hindus." The court also refused to accept Lt Col Purohit's contention that he had attended the meetings as part of a "covert military intelligence operation".
The Army officer, however, argued that the NIA was "selective" in exonerating some of the accused, adding that he was made a "scapegoat" in the case. He also said that the statements of witnesses against him were fabricated.
Last year, Lt Col Purohit wrote to then Defence Minister Manohar Parrikar, claiming he had been falsely implicated in the case. "I have been robbed of honour, dignity and rank and punished for serving the nation," the letter read.
Lt Col Purohit was commissioned into Maratha Light Infantry in 1994. Between 2002-2005, he served in the counter-terrorism operations unit in Jammu and Kashmir before being shifted to Military Intelligence.