The entire case and the investigation was carried out by NIA to malign one political group, Swami himself later said the confessions were under torture, and he retracted them. In fact independent investigations by the U.N, and the U.S declared that Pakistan based group, the LeT was behind the attack
Refer:
The Statesman: Is India blind and deaf?
The Samjhauta Train terror is crucial for alleging Hindu involvement in order to put Pakistan and India on the same footing insofar as cross-border terror is concerned. It was in this act that Pakistani citizens and not merely Indian Muslims became victims. That is why a Pakistani Minister in November 2011 visiting India could quote the Samjhauta blast to demand that like the 26/11 terrorists Hindu terrorists should also be nailed and punished.
The problem as repeatedly cited is of course that a UN Security Council Resolution had already indicted Lashkar-e-Taiba for the Samjhauta terror. This followed a detailed probe by the American FBI which identified and named all the four operatives from Pakistan who carried out the act. That is why the UN banned the Lashkar as a terrorist organization. The UN named Hafiz Saeed as the mastermind behind the operation and imposed sanctions against him. The sanctions could not be implemented because China exercised its veto power to protect Hafiz Saeed. This has been reported in these columns half a dozen times but to no effect. Neither the NIA, nor the politicians nor the media care to explain this glaring contradiction. The entire political and media establishment blissfully continue with allegations of Hindu terror in the Samjhauta blast as of the UN does not exist.
Samjhauta Blast Case: Counter Investigation To NIA Investigation -The New Indian Express - a very long and step by step counter to the inexplicable investigations of the NIA
Again during election time, there was an "interview" of Swami published in some pro-congress mouth pieces where he discussed his involvement, which was later revealed to be fake.
It is not just this, he was also accused in the Mecca masjid blast, and then later it was found that the group; was again an islamic group called the HuJI.
Refer:
HuJI ban takes no note of 'Hindu terror' role - The Times of India
‘Huji, not Hindu group, behind Mecca Masjid blast’ - Hindustan Times
Overall there has been a huge attempt to make him loook like a Hindu Osama of some sort, but it has failed, but parties and certain sections of the media completely ignore it and continue their tirade against this nonsense.
Even the now infamous 26/11 was ready to be painted as "Hindu Terror".
David Headley bought saffron wrist bands to try and paint the whole thing as hindu terror
With sacred threads, Abu Jundal tried to colour 26/11 saffron - The Times of India
Later a book was released, that had a congress person at the launch:
RSS & 26/11: Digvijaya flags it off again, this time in Mumbai - Indian Express -26/11, An RSS Conspiracy?
Luckily catching Kasab alive really prevented any sort of nonsense from occurring.
It doesnt end here, there are many cases where when terrorists were caught, politicians would create doubts about the terrorist and tried to show the police in bad light. If there was an encounter, the media and certain parties would constantly try to show the that terrorists were "innocent" while demonizing the policemen and so on....
I dont even know if this is just congress stupidity in going to an extreme with the politics of appeasement of one community for votes, or if they were genuinely compromised. Seems like a combination of both. It really , really hurt our ability in fighting terror, when every single nutty conspiracy theory was not just given importance but made mainstream and entire investigations were subverted by it.
