The Central Bureau of InvestigationChandan Khanna/AFP/Getty Images

For special CBI Judge S J Sharma, acquitting all 22 accused in the alleged fake encounter killings of gangster Sohrabuddin Shaikh, his wife Kausar Bi and his aide Tulsi Prajapati on Friday, was the last judgment of his career.

"This is my last judgement...," said the judge, who is set to retire later this month, in his ruling. "It is unfortunate that a family (of victims) has lost a son, brother...But the evidences were not enough to show that these accused were authors of the crime."

The judge said he felt sorry for the families of Shaikh and Prajapati as "three lives were lost". But the system demands that the court go solely by evidence, he added. All the accused, who were mostly police officials from Gujarat and Rajasthan, were out on bail during the years-long trial.

The 13-year-old case saw several twists and turns, including 92 prosecution witnesses turning hostile. At one point, BJP president Amit Shah was also arrested briefly in 2010. The three victims who were returning to Sangli in Maharashtra from Hyderabad in a bus were taken into custody by a police team on the night of November 22-23, 2005.

The couple were taken in one vehicle and Prajapati in another. The CBI, which was the prosecuting agency, said Shaikh was killed on November 26, 2005, allegedly by a joint team comprising Gujarat and Rajasthan police, and Kausar Bi three days later.

Prajapati, who was lodged in an Udaipur central jail, was killed in an encounter on the Gujarat-Rajasthan border on December 27, 2006. Of the 22 accused, 21 are junior-level police officials from Gujarat and Rajasthan, who the CBI said were part of the teams that abducted the three and later killed them in staged encounters.

The remaining accused was the owner of the farm house in Gujarat where Shaikh and Kausar Bi were illegally detained before they were killed.

"The prosecution has failed to put forth any documentary or substantive evidence to suggest or establish the conspiracy theory against the 22 accused. It has failed to establish all charges levelled against them.

Hence all the accused stand acquitted," the judge said in his judgement. The court cannot rely solely on "circumstantial and hearsay evidence", he added. Police said Sohrabuddin was linked with terror groups like Lashkar-e-Taiba and was allegedly conspiring to assassinate Prime Minister Narendra Modi, who was then the chief minister of Gujarat.

The case was initially probed by the Gujarat CID before the CBI took over in 2010.

The Supreme Court in 2013 directed that the trial be shifted to Mumbai from Gujarat on the central agency's request to ensure a fair trial.