[3] The Nanavati-Mehta Commission, appointed by the state government in the immediate aftermath of the event, concluded in 2008 that the burning was a pre-planned act of arson committed by a thousand-strong Muslim mob.
[5] In contrast, the Banerjee Commission, a one-member panel instituted in 2004 by then Rail Minister Lalu Prasad Yadav of the Ministry of Railways, characterized the fire as an accident in its 2006 report.
[11] In February 2002, thousands of devotees of Rama (known as "Ramsevaks" or "Kar Sevaks") traveled from Gujarat to Ayodhya at the behest of the Vishva Hindu Parishad to participate in a ceremony called the Purnahuti Maha Yagna.
[14] J. Mahapatra, the Additional Director General of Gujarat Police, stated that "miscreants had kept petrol-soaked rags ready for use much before the train had arrived at Godhra.
"[15] In September 2008, the Nanavati-Mehta Commission submitted the first part of its report, which concluded that the burning of the S-6 coach of the Sabarmati Express near Godhra railway station was a "planned conspiracy.
[21][22] Historian Ainslie Thomas Embree stated that the official account of the train attack—that it was organized and carried out by people under orders from Pakistan—was entirely baseless.
[23] Scholar Martha Nussbaum similarly challenged this narrative, stating that several inquiries found the fire to be the result of an accident rather than a planned conspiracy.
Additional director general of police G. C. Raigar had informed prior to the Godhra train burning that the Vishwa Hindu Parishad (VHP) activists could instigate communal violence.
[25][26] A study conducted by the Gujarat Forensic Science Laboratory concluded that the fire was caused by inflammable liquid poured into the coach by the attackers.
[29] However, Shah's alleged closeness to Narendra Modi drew sharp criticism from victims, human rights organizations, and political parties, leading to demands for the appointment of a Supreme Court judge.
[35] The report identified Maulvi Husain Haji Ibrahim Umarji, a cleric in Godhra, and Nanumiyan, a dismissed Central Reserve Police Force officer, as the "masterminds" behind the operation.
[38][39] The Communist Party of India (Marxist) and the Indian National Congress objected to the commission's exoneration of the Gujarat government, citing the timing of the report—just months before general elections—as evidence of unfairness.
Congress spokesperson Veerappa Moily criticized the premature absolution of the Gujarat government for its alleged complacency in the carnage before the commission's second and final report was released.
[40] The commission has also been heavily criticized by academics, such as Christophe Jaffrelot, for obstructing the course of justice, supporting the conspiracy theory too quickly, and allegedly ignoring evidence of governmental complicity in the incident.
In September 2004, two and a half years after the train burning, Yadav appointed former Supreme Court Justice Umesh Chandra Banerjee to investigate the incident.
It declared the formation of the investigation to be a "colorable exercise of power with mala fide intentions" and deemed the argument of an accidental fire to be "opposed to the prima facie accepted facts on record."
[53] Lalu Prasad Yadav, then the Minister for Railways, cited the report as evidence that the Narendra Modi government had orchestrated the riots that followed, calling it an exposure of the BJP.
[54] On 17 March 2002, chief suspect Haji Bilal, a local town councillor and Congress worker,[55] was captured by an anti-terrorist squad in Godhra.
It ordered the SIT to serve as the nodal agency for witness protection, file supplementary charge sheets, and potentially cancel the bail of the accused.
[59] The death penalty was awarded to 11 convicts, including those believed to have attended a meeting the night before the incident where the conspiracy was formed, and those who, according to the court, entered the coach and poured petrol before setting it on fire.
[76] BJP spokesperson Shahnawaz Hussain stated, "The theory propagated by the (central) government and some NGOs (Non-Governmental Organization) has been proved wrong...."[77] Law Minister Veerappa Moily, a Congress Party member, said it was premature to comment and that the courts would take their own course.
BJP spokesperson Ravi Shankar Prasad added that the verdict had exposed the "nefarious designs" of the UPA government, which he accused of trying to cover up the entire episode.