Justice Harsha Devani dismissed Pandey's prayer, saying he an absconder despite being a top police officer of additional DGP rank, his plea should not be entertained.
The court also said a cognizable offence is made out in the FIR and adequate proof exists as three out of four accused persons were in prior custody of police.
The court also noted that since the CBI is in the last stage of filing the charge sheet the time is not appropriate for quashing the complaint.
Countering Pandey's argument that his role in the case was limited to providing intelligence inputs, Additional Solicitor General Indira Jaising had told the court that Pandey was the "mastermind" behind the killing of four people, including Ishrat.
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"He is the mastermind behind the whole encounter. He was a conduit... He received inputs, passed it to his subordinates and arranged everything... In fact, he was in total control of the operation. He actually acted as Rambo," she had alleged.
Pandey, as Joint Commissioner of Police, Ahmedabad, was heading the Crime Branch when Ishrat, Javed Shaikh alias Pranesh Pillai, Amjadali Akbarali Rana and Zeeshan Johar were killed in the alleged encounter near here on June 15, 2004.