The acquittal of Swami Aseemanand and his three associates for the Delhi-Lahore Samjhauta Express explosion near Panipat in February 2007, when 68 persons were killed and many others injured, is bound to be seen as travesty of justice. Many of those, who were victims and the survivors were expecting justice in the form of punishment to the accused in the long-drawn prosecution of three right wing activists have expressed their disappointment over the outcome of the case. In fact, many of those, who survived in the explosion case were mainly Pakistani citizens, had lost hope of getting justice when the case was pending for a pretty long time. But any acquittal in a heinous crime is likely to raise many questions about the credibility of the investigation process or the effectiveness of the prosecution system in the country. There are many cases of similar nature in which the outcome may also spark cynical questions ranging from attribution of political motives to suspicions of institutional biases. The Samjhauta Express explosion case in which citizens of both India and Pakistan were killed may evoke all such responses. In fact, it is also surprising that many of the witnesses from both India and Pakistan could not depose before the court when the prosecution process was going on. The outcome at present casts shadow on India and its agencies’ ability and resolve to investigate and prosecute major acts of terrorism. It is the perhaps the third case in which Swami Aseemanand has been acquitted. He was earlier cleared of involvement in the Ajmer Dargah blast, which killed three persons in October 2007, and the Mecca Masjid blast that left nine dead in Hyderabad in May 2007. Aseemanand alias Naba Kumar Sarkar, was a key figure, according to the prosecution, behind a Hindu right-wing group that wanted to avenge incidents such as the Akshardham temple massacre of 2002. The contours of ‘saffron terror’ were disclosed by Aseemanand in 2010 when he gave a lengthy statement before a magistrate, detailing the planning and execution of some key terrorist attacks between 2006 and 2008. This confession failed to convince the trial courts, mainly because of his subsequent retraction. That he was in police custody at the time also cast a doubt whether it was voluntary or not. But one thing is certain that before his arrest, the law enforcing agencies in this case failed to lay their hands of Swami Aseemanand and his associates till all the evidence was collected for implicating him in the ‘saffron terror’ case. Looking at the history and run up to the events that led to explosions at different places in 2007 after the Samjhauta Express blast, there is no doubt that these terror incidents were aimed at destroying all attempts to build friendly relations between India and Pakistan. It is also possible that extremists of any hue may have been behind such incidents in India and planning more such incidents. It is a public knowledge that such organization to which Swami Aseemanand owed his allegiance were conspiring to targets members of a particular community to create terror and instill a sense of fear through such incidents. It is unfortunate that the change of regime at the Centre in 2014 seemed to have weakened the National Investigation Agency’s resolve to deal stringently with such cases. Details of the verdict are not yet available, but it is clear that the prosecution case collapsed after key witnesses turned hostile. On the flip side, the fact that some early suspects were Muslims and that the United States of America and the United Nations had linked Lashkar-e-Toiba operatives such as Arif Qasmani to the blasts could have been important factors. The larger concern for the criminal justice system is whether such acquittals indicate innocence, or the prosecution’s lack of freedom and resolve to obtain a conviction. If the NIA had slowed down its investigation process against these accused under pressure from the rulers of the day, then there is every likelihood that all other cases of similar nature will suffer from the same fate putting a big question mark on the working of the probe agencies and prosecution process in India.