The case of Mr. Zapata would usually be overlooked in the flood of 50,000 Bronx misdemeanor filings a year. But he was part of a special legal-defense effort led by the Bronx Defenders, which provides legal representation to poor Bronx residents charged with crimes. That effort tested the borough’s courts by trying to bring 54 misdemeanor marijuana possession cases to trial for clients who had been arrested as part of New York City’s controversial stop-and-frisk program and wanted to fight the charges.

Instead, these defendants got a through-the-looking glass criminal justice system where charges that were punishable by a maximum sentence of three months in jail could take many times that just winding toward an always elusive trial. And when the increasingly elastic speedy-trial rules of the Bronx were finally stretched too far by delay after delay, prosecutors would sometimes drop the cases as if they were never quite worth their time anyway.

Eventually, the effort by the Bronx Defenders, done in partnership with the Wall Street law firm Cleary Gottlieb Steen & Hamilton, was scrapped. The grim conclusion was that the borough’s courts were incapable of giving defendants the hearings that people expect. Of the 54 cases, not one ended in a trial.

“The normal rules about being ready and having your day in court just don’t apply,” said Lev L. Dassin, a former acting United States attorney in Manhattan who was the Cleary Gottlieb partner in charge of the firm’s work on the project. “It’s appalling.”

The rights of the accused were not the only ideals compromised. The inability to get a judge to provide a complete hearing or a full decision in a single case meant the Bronx courts ignored pressing constitutional questions about the city’s controversial stop-and-frisk program. There were no hearings that allowed Bronx judges to wrestle with the fraught issues of public safety versus civil liberties, and no rulings that provided the police with firm guidelines about what the Constitution allowed when someone was searched in the street.