The encounter killing was not exposed until a media report made a year later. This report, together with a petition filed in the Supreme Court by Sheikh's brother, led to investigations into the incident. In April 2007, senior state police officers were arrested for their connection to the case.
Media report and Supreme Court petition The encounter killing was exposed after a few police inspectors boasted about it over drinks with the journalist Prashant Dayal, who conducted his own investigations at the farmhouse, and then at
Ilol. He ascertained that a burqa-clad woman had been cremated there. He then broke the story in November 2006, in the leading
Gujarati newspaper,
Divya Bhaskar, and gave details of the encounter. Meanwhile, Sheikh's brother Rubabuddin petitioned the Supreme Court claiming that the Gujarat police had orchestrated the encounter and demanded to be given information on the location of his sister-in-law Kauser. In March 2007, the Supreme Court ordered the state Criminal Investigation Department to conduct a time-bound investigation. Inspector-General
Geetha Johri was given the task of conducting the investigation, and was to report directly to the court. She gathered evidence that implicated the role of several police officers in the encounter. However, it has been claimed that she may have "steered clear of linking them to a political conspiracy". Based on the evidence collected by Johri, DIG Police Rajnish Rai on 24 April 2007, arrested DIG (Border Range) D G Vanzara and Rajkumar Pandian, Superintendent of Police with the Intelligence Bureau, and
M.N. Dinesh of Rajasthan police, who is alleged to have been working at the behest of the marble lobby. The Supreme Court asked the Gujarat government to place before it the inquiry reports prepared by Johri, which had allegedly said that Sheikh was killed in an encounter killing. Johri was removed from the investigation after this report was published. On 3 May 2007, the court asked the government whether Johri had been dismissed from the investigation so that a further probe would not be carried out, and directed it to submit a final report on 15 May, the day scheduled for the final order.
Inspector General's report In Part B of the report, Johri recorded facts relating to repeated attempts by the accused police officers and Amit Shah to sabotage the Supreme Court mandated enquiry. The report states that Shah "brought to bear pressure" on the enquiry process, with the result that Ms. Johri was directed to suspend the enquiry and the enquiry papers were taken away from her "under the guise of scrutiny." Johri also records that Shah even "directed Shri G.C. Raigar, Additional Director General of Police, CID (Crime & Railways) to provide him with the list of witnesses, both police and private, who are yet to be contacted by CID (Crime) for recording their statement in the said enquiry." Not finding the Gujarat government's explanations satisfactory, the bench of Justices Tarun Chatterjee and P.K. Balasubramanyam ruled that Johri would report directly to the Supreme Court. She was reinstated in the same position and also asked to head the case. ==Allegations of involvement in Haren Pandya murder==