Court records filed Thursday warned of possible retaliatory strikes against witnesses who will testify against both men.
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El Chapo Guzman extradited to New York last month followed by one of his most trusted allies, Jesus Beltran Leon, who was moved by American law enforcement from the Mexico City airport to Chicago.
Leon was in the federal lockup in the Loop Thursday while his former boss, El Chapo, was in the sister facility in Manhattan.
According to a court filing in New York, prosecutors are concerned about trial evidence against El Chapo and his operatives getting into public view, and possibly even in the hands of "hitmen, who carried out hundreds of acts of violence, including murders, assaults, kidnappings, assassinations and acts of torture at the direction of the defendants." According to prosecutors: "the defendants directed and ordered these acts of violence."
Government lawyers in New York and Chicago asked the courts to impose strict guidelines on the "discovery" process of evidence sharing between attorneys. They want only a small circle of attorneys to have access to the evidence.
"Statements by cooperating witnesses who are regarded as 'snitches' or 'rats' by their criminal associates...Pose obvious dangers according to a filing by federal prosecutors in New York," they said.
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A similar request to lock down evidence in Chicago was approved Thursday by Chief U.S. District Court Judge Ruben Castillo in the Leon case.
Both men will face the same prime witnesses - the Flores brothers.
Pedro and Margarito Flores are twins from Chicago's Little Village neighborhood who became top allies of drug lord El Chapo and his multi-billion dollar network of cocaine traffickers.
Little did Chapo and Leon know that as the feds closed in, Chicago's Flores twins decided to turn on the cartel; secretly recording conversations with Chapo and other cartel leadership.
The Flores brothers would testify how cartel bosses used jumbo jets, submarines, trucks and tunnels to smuggle tons of drugs into the U.S. The Flores' already pleaded guilty, got 14 years, and are in witness protection. El Chapo is due in court Friday morning in New York. Prosecutors wanted him to appear by closed circuit video-the judge Thursday ordered him physically present in court.