Rubabuddin's lawyer Gautam Tiwari alleged that the prime accused, senior Gujarat anti-terrorism squad officials D G Vanzara and Rajkumar Pandian, and Rajasthan IPS officer Dinesh MN, who were all discharged in the case, conspired to execute the fake encounters.
Mr Tiwari, arguing against the discharge of Dinesh MN, claimed the officer, who was the superintendent of police, Udaipur, in November 2005, went to Ahmedabad to meet other police officers who were "part of the conspiracy" to arrest and kill Sohrabuddin and his wife.
While the officer claims to have visited Ahmedabad for official training, none of his superiors, including the inspector general of Rajasthan police, know of any such training scheduled at the time, Mr Tiwari said.
"Besides, Dinesh MN claims to have received information on Sohrabuddin and says he had gone to arrest him since he was wanted in a case in Udaipur. Then why did Dinesh MN not take along police officers concerned? Instead, he took with him three junior officers who were part of his coterie," the lawyer said.
"There is evidence in the form of witnesses' statements to establish that Mr Dinesh, along with Mr Vanzara and Mr Pandian, played an integral role in conspiring for and executing the encounters," he said.
Mr Tiwari said after Sohrabuddin and Kausar Bi's killings, Mr Prajapati was brought to Udaipur Central jail where he repeatedly voiced apprehension of threat to his life, and even wrote to the National Human Rights Commission.
Mr Prajapati's complaint to the NHRC was also probed by Dinesh MN, the lawyer said.
Several inmates of Udaipur prison later testified that Mr Prajapati had no plans of escaping from police custody and he feared that Dinesh MN and others would kill him in a fake encounter, the lawyer said. Police had later claimed that he escaped while being taken to court.
The Bombay High Court is conducting day-to-day hearing on petitions filed by the CBI and Rubabuddin Shaikh challenging the discharge of several police officers.
Sohrabuddin, a gangster with alleged terror links, was killed in an alleged fake encounter by the Gujarat police in November 2005. His wife disappeared mysteriously, and was also alleged to have been eliminated by police. Mr Prajapati, a witness to these killings, was killed in another alleged fake encounter by the Gujarat and Rajasthan police in December 2006.
Of the 38 people charge-sheeted by the CBI, 15, including police officers D G Vanzara, Rajkumar Pandiyan, Dinesh MN, and BJP president Amit Shah, who was minister of state for home in Gujarat when these alleged fake encounter killings took place, were discharged by the special CBI court in Mumbai between August 2016 and September 2017.