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For years, Juan Carlos Bonilla, better known as "El Tigre," was a feared figure in Honduras. His roots were in the military and he brought that bearing to the National Police that he ultimately led.

But Bonilla’s tenure was plagued by allegations of human rights violations, including running death squads and being a hired killer for drug traffickers. On Tuesday, nearly two years after he was extradited to the United States, he pleaded guilty to drug trafficking in a federal court in New York.

By pleading guilty to a single drug trafficking charge, Bonilla avoided a trial scheduled to begin Monday and likely a much longer sentence. His plea also dramatically darkened the landscape for former president Juan Orlando Hernández, who had been his co-defendant.

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U.S. District Judge Kevin Castel confirmed Wednesday that Hernández’s trial would begin Monday.

The other co-defendant, Mauricio Hernández Pineda, Hernández’s cousin, also pleaded guilty last week. Their pleas leave the former president alone for Monday’s trial and potentially become star witnesses for the prosecution.

Juan Orlando Hernández

Former Honduran President Juan Orlando Hernández is escorted in handcuffs ahead of his extradition to the U.S., Tegucigalpa, Honduras, April 21, 2022. (AP Photo/Elmer Martinez, File)

"It reinforces the accusatory thesis that it is an organized structure made up of three perpetrators who are on trial and who had roles in the drug trafficking conspiracy," said Honduran lawyer Marlon Duarte.

Duarte said Hernández will have to consider his own plea. It’s unclear, however, whether prosecutors would still be willing to offer him a deal.

Hernández was extradited to the U.S. in April 2022, just three months after leaving office, and faces drug trafficking and weapons charges. He had maintained his innocence, saying the allegations were revenge from drug traffickers he had extradited to the U.S.

U.S. Attorney General Merrick Garland said at the time that Hernández "abused his position as President of Honduras from 2014 through 2022 to operate the country as a narco-state."

Bonilla was a component of that operation, according to prosecutors.

U.S. prosecutors in Manhattan announced charges against Bonilla in April 2020, alleging that he used his law enforcement clout to protect U.S.-bound shipments of cocaine. Bonilla denied at the time being a drug trafficker.

There was a time when Hernández and Bonilla were considered U.S. partners in the drug war.

Bonilla was named head of Honduras’ National Police in May 2012 by President Porfirio Lobo, through December 2013. He was removed when Hernández took over as president. Hernández’s rise to lead Honduras’ congress and then to run for president was fueled in part by drug money, prosecutors allege.

Prosecutors have said Bonilla let drug shipments pass through police checkpoints without inspection and gave drug organizations information about police aerial and maritime interdiction operations so they could evade them.

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An internal police report in Honduras once accused Bonilla of leading death squads and participating in three killings or forced disappearances between 1998 and 2002. He was prosecuted for one murder but was acquitted in 2004.