During his tenure as the Chief Justice of India, Khare was confronted with the failure of the justice system in the aftermath of the Gujarat violence following the Godhra train burning. His decision to reopen the Best Bakery Case provided some recourse for victims of the violence. Speaking to The Hindu newspaper when he retired he said, "I found there was complete collusion between the accused and the prosecution in Gujarat, throwing rule of law to the winds. The Supreme Court had to step in to break the collusion to ensure protection to the victims and the witnesses. I was anguished and pained by the turn of events during the trial of the riot cases but was determined to salvage the criminal justice delivery system."