CHICAGO — A Chicago man who spent more than a decade in prison on a drug conviction filed a federal lawsuit Thursday alleging he was framed by a corrupt city police sergeant and his crew.

Ben Baker was freed earlier this year after he petitioned for a new trial and Cook County prosecutors dropped the charges against him. The case was dismissed because the primary witness in the case, former Chicago police Sgt. Ronald Watts, was convicted in 2013 of extorting protection payoffs from drug dealers.

“This case is going to be about exploring the code of silence, how it happens and how it continues to happen to this day,” Baker’s attorney, Joshua Tepfer of the Exoneration Project at the University of Chicago Law School, said. “It is very much alive and well.”

“We have not yet received the lawsuit and cannot comment,” said city law department spokesman Bill McCaffrey.

Baker, 44, alleges in his lawsuit — which names Watts and his partner Kallatt Mohammed and others still working for the department — that he was targeted because he refused to pay Watts a protection payoff of $1,000 in order to deal drugs at a public housing complex.

Baker claims in retaliation, Watts and his crew tried to tie Baker to heroin found in a mailbox at the Ida B. Wells public housing complex. Baker was found not guilty in that case, and months later was arrested by Watts’ crew after the officers claimed he was found inside a building at the housing complex with heroin in his pocket packaged for sale.

Baker was out on bond in that case when he complained to Chicago police internal affairs about Watts’ corruption.

The lawsuit contends that after learning of Baker’s complaint, members of Watts’ crew framed him and his fiancee in a separate drug case months later.

In his petition earlier this year for a new trial, Baker and fiancee, Clarissa Glenn, contended Watts had planted a plastic bag filled with heroin in their vehicle after it was stopped by the sergeant and another officer. In the petition, the couple said they decided to plead guilty due the possibility of a 30-year prison sentence and fears their children would be left alone.

Baker, who had previous criminal convictions on his record, was sentenced to 14-years in prison. Glenn, who had no criminal record, was given probation.

At the time of Baker’s arrests, an investigation of Watts and his crew was “well underway” by the FBI, with the knowledge of the police department’s Internal Affairs Department, according to the lawsuit.

It was in 2011 that Watts and Mohammed were caught in an FBI sting attempting to steal from an FBI informant $5,200 of what they believed was drug money. Mohammed was convicted of theft and sentenced to 18 months in prison.

The case against Watts was built in part on the undercover work of two whistleblower officers, Shannon Spalding and Daniel Echeverria. The pair later filed a lawsuit of their own alleging they were blackballed by police brass and moved to do-nothing jobs in retaliation for their undercover work. The lawsuit was settled on the eve of trial in May for $2 million.