For the first time since the early 2000s, staffers from the Cook County state’s attorney’s office will handle a case tainted by the involvement of the former late Chicago Police Cmdr. Jon Burge.

Judge LeRoy K. Martin Jr., presiding judge of the criminal division, on Thursday assigned the state’s attorney to review a petition for a certificate of innocence by James Gibson, who was set free from a life sentence for a 1990 double-murder. Gibson was released from prison based on allegations that he was tortured by detectives working under Burge.

The state’s attorney’s office will take the matter over from special prosecutors who were working under Robert Milan. Milan, this spring, grudgingly dropped charges against Gibson after he was granted a new trial.

“For four years of litigation, I have fought the special prosecutor and won every time,” Gibson said outside the courtroom. “Kim Foxx is a fair state’s attorney. I believe I will get a fair shake.”

A certificate of innocence is granted by the court as formal recognition of a wrongful conviction and entitles a former defendant to clear his or her record, access to free counseling services and a payout of as much as $200,000 from the state.

Milan had said he only dropped the charges because witnesses against Gibson had either died or were no longer cooperative. Milan said did not believe Gibson was the victim of a wrongful conviction and had intended to oppose his bid for a certificate of innocence.

Martin did not rule Thursday on whether special prosecutors would continue to handle the case of Tony Anderson, who remains in prison for a conviction he said was based on a false confession tied to Burge-era detectives. Anderson is approaching the date for a hearing he was awarded by the state Torture Inquiry and Relief Commission in 2013.

Assistant State’s Attorney Carol Rogala said Thursday that her office would be “starting from scratch” in their review.

Special prosecutors had been assigned to Burge-related cases since 2002, after a judge ruled that then-State’s Attorney Richard Devine had a conflict of interest because he had represented Burge when working at a private law firm. Milan is the third private attorney to serve in the role in the years since, but attorneys for another Burge torture victim, Gerald Reed, had tried to have him removed from handling the cases, arguing Milan had been a top deputy under Devine and that prosecutors from private firms had a financial incentive to press on with prosecutions and continue billing the county for their services.

Martin seemed unconcerned about the special prosecutors’ power to take on criminal prosecutions or Milan’s involvement. But in a surprise move last month, Martin ruled that the conflict of interest stemming from Devine’s role as the county’s chief prosecutor was no longer an issue and began a review of all pending Burge cases, which total about 25 to 30.