Ben Baker had long been a thorn in the side of corrupt Chicago police Sgt. Ronald Watts, who framed the part-time drug dealer on a narcotics charge in retaliation for refusing to pay a protection payoff of $1,000, court records show.

While Baker was on bond awaiting trial in December 2005, he and his wife, Clarissa Glenn, were stopped by Watts and one of his team members. Once again, the officers claimed they found a bag of heroin in Baker’s car and tagged the couple with major felony drug charges, according to the court records.

Faced with up to 15 years in prison and frightened that their young children would be left without parents, the couple copped deals with prosecutors in order to spare Glenn from prison. Baker, though, had an additional two years tacked on to his sentence for the other drug case — a total of 14 years behind bars.

Now Baker and Glenn are seeking to have those guilty pleas thrown out, claiming in a court filing last week that Watts had planted the heroin — this time as retribution for blowing the whistle on him. Watts had been tipped off that Baker had gone to the Chicago police internal affairs division about his earlier shakedown, records show.

To buttress their claim, the couple has produced court records that show the judge who took their guilty pleas in September 2006 was already aware that Watts’ crew was under investigation, according to the petition filed in Cook County Criminal Court.

In fact, Judge Michael Toomin told the couple that if the allegations were ever proved, they could come back to court and he would gladly throw out their cases.

The court filing marks the latest fallout over the corrupt squad led by Watts, who in 2012 was charged along with one of his underlings, Officer Kallatt Mohammed, with shaking down a drug courier who turned out to be an FBI informant. Both were convicted and sentenced to federal prison.

Baker was freed in January after serving more than a decade of his 14-year sentence. Cook County prosecutors agreed to drop the original drug charge against him after his lawyer, Joshua Tepfer, revealed dozens of pages of court and law enforcement records showing that police internal affairs had been aware as far back as the late 1990s of corruption allegations involving Watts’ team — yet failed to take them off the street.

At the time of Baker’s arrest, Watts and his entire crew also were the target of an ongoing FBI investigation, according to records uncovered by Tepfer, of the Exoneration Project at the University of Chicago Law School. One FBI report from September 2004 showed that an informant had told federal agents that Watts and other officers were routinely shaking down drug dealers for thousands of dollars in cash in exchange for police protection at the Ida B. Wells public housing complex.

But it wasn’t until five years later that agents were able to build a criminal case against Watts and Mohammed, based in part on the undercover work of two whistleblower officers, Shannon Spalding and Daniel Echeverria.

Tepfer told the Tribune on Friday that the latest filing shows how Watts and his crew were able to terrorize a community for years with their illegal schemes, using their police powers to keep the largely poor and vulnerable people who lived in Ida B. Wells in line.

“These cases were brought by vindictive and corrupt police officers who were framing individuals for things that they did not do,” Tepfer said. “(Baker and Glenn) are likely just the tip of the iceberg when it comes to victims of the decadelong criminal enterprise headed by Sgt. Watts.”

The experience was particularly rough on Glenn, a churchgoing mother of three who had never been arrested before and has not been since, according to her lawyer, Jonathan Brayman.

“Every step of the way, Clarissa has told anyone who would listen that she and Ben were innocent,” he said.

According to the petition, Baker and Glenn were stopped by Watts and Officer Alvin Jones on Dec. 11, 2005. Jones claimed in police reports that as he walked up to the car he saw Glenn hand a clear plastic bag filled with heroin to Baker, who put it in the driver’s-side console.

But Baker and Glenn claimed Watts had pulled the bag out of his sleeve and placed it in the car after a search had turned up no drugs. Back at the Wentworth District police station, Jones and several other members of Watts’ team typed up a false report, adding officers as witnesses who weren’t even at the scene, the couple alleged.

Before the couple pleaded guilty, Judge Toomin acknowledged in court that he had been shown reports that indicated Watts’ crew had been under investigation by internal affairs and that a prosecutor with the state’s attorney’s office’s public integrity unit was involved. But there had been no concrete evidence of wrongdoing and no move by prosecutors to drop the charges, so the judge said he couldn’t do anything with the information, according to a transcript.

“Let me say this to both of you,” Toomin told Baker and Glenn, according to a transcript. “There has not been sufficient showing to me that these are renegade police officers, that they are bad police, that they are outlaws.”

But, Toomin said, “police officers do get charged with doing things that are wrong, breaking the law.”

“If that should happen here in this case, I would have no hesitation,” the judge said. “I would toss out these convictions.”