When a former Honduran congressman goes on trial next week in Manhattan, charged with conspiring to import cocaine into the United States, his older brother will be absent from the courtroom but will loom large over the case.
That older brother, Juan Orlando Hernández, is the president of Honduras, and an ally of President Trump on immigration and security, which are Washington’s top priorities in the region.
But even as President Hernández agreed on Wednesday to a deal that will allow the United States to force some migrants to seek asylum in Honduras — a cornerstone in Mr. Trump’s plan to curb migration — federal prosecutors were preparing to present evidence that the Honduran president was a member of the drug trafficking conspiracy his brother was charged in.
President Hernández, his younger brother, Juan Antonio (Tony) Hernández — the man facing trial — and other politicians and law enforcement officers were all part of a “broader criminal plan” to use drug trafficking “to help assert power and control in Honduras,” the prosecutors wrote in an Aug. 2 filing in Federal District Court.
They said that the president used drug money to help win elections in 2013 and 2017, and that he offered protection to drug traffickers who supported him. They said President Hernández also considered eliminating a Honduran law that allowed for the extradition of traffickers — a law that he had himself pushed through Congress when he led that body — because he feared the United States would try to extradite his brother, the court filing shows.
President Hernández has not been charged in the case, and prosecutors do not use his name in court papers, labeling him only as CC-4, for co-conspirator No. 4. But they leave no doubt about his identity: “CC-4 was elected President of Honduras in late 2013,” the prosecutors wrote.
After the allegations became public in the court filing last month, protesters in Honduras, where the president is increasingly unpopular, renewed their call for his resignation, with many adding CC-4 alongside the president’s initials — J.O.H. — to the signs that appear at every rally calling on him to resign.
President Hernández, 50, has vigorously denied any involvement in the drug crimes.
As the date of the trial approached, President Hernández offered television interviews, asserting that his conscience was clear. The allegations, he told one interviewer last week, were made by people seeking favorable treatment from the court. Their statements, he said, “don’t have the slightest value, and that will be demonstrated in the trial.”
He blamed the allegations against him on revenge by traffickers who oppose his strong antidrug policies.
“All Hondurans know that we have led an unprecedented battle to free the country from the control of drug traffickers,” President Hernández said on Aug. 3 in response to news reports about the prosecutors’ memorandum. “We have worked in an effective and close alliance, a very productive one, with the government of the United States.”
On Wednesday, President Hernández delivered again on that close alliance with the United States, signing the migration deal. The agreement is similar to one that Washington pressed on Guatemala and El Salvador as part of the Trump administration’s drive to stop migrants from asking for asylum in the United States.
The deal won President Hernández a handshake with Mr. Trump during the United Nations General Assembly, sending a message to Hondurans that Washington now appears to care less about drug trafficking than about halting migrants.
Kevin K. McAleenan, the acting secretary of Homeland Security, heaped fulsome praise on President Hernández. In a tweet, he called the president “a strong partner” who was working to “combat irregular migration and transnational criminal organizations.”
The government’s allegations about President Hernández are the latest turn in a lengthy drug trafficking investigation by the United States attorney’s office in Manhattan and the Drug Enforcement Administration that has exposed corruption at the highest levels in Honduras, a nation of about nine million people that is also home to an American military base.
The country, plagued by violent drug gangs that have generated one of the highest homicide rates in the world, has become a gateway for huge amounts of cocaine moved through Mexico and into the United States. Honduras is also the first landing point for about 80 percent of suspected drug flights leaving from South America, the State Department has said.
In recent years, federal prosecutors have charged at least seven officers of Honduras’s national police force; the son of the country’s previous president; several members of the Rosenthal family, a prominent Honduran banking and political family; at least two former Honduran mayors; and three former Honduran congressmen, including Tony Hernández, the president’s brother.
At a 2017 sentencing of one defendant, a prosecutor said the evidence showed nothing short of “state-sponsored drug trafficking.”
Tony Hernández, 41, has pleaded not guilty to the charges. If convicted, he could face life imprisonment. His lawyer, T. Omar Malone, recently told Judge P. Kevin Castel in court that his client’s case could be hurt if the trial ended up litigating “the geopolitical history of Honduras.”
Prosecutors, in their recent filing, said President Hernández, his brother and other co-conspirators “relied on drug proceeds to fund National Party campaigns and other political operations, to control large swaths of the Honduran government, to bribe officials who helped ensure safe passage for their cocaine, and in an effort to protect themselves from law enforcement scrutiny in Honduras and elsewhere.”
President Hernández, like his predecessor, Porfirio Lobo, “was elected president based at least in part on the proceeds of drug trafficking,” the prosecutors wrote. Mr. Lobo has not been charged.
The memorandum outlined four occasions in which an accused Honduran drug trafficker, who was also an official in the president’s National Party, said he had paid bribes to or for President Hernández and Mr. Lobo in exchange for protection.
According to the memo, the trafficker sent $2 million to Mr. Lobo to help fund his 2009 presidential election. Mr. Lobo recently denied receiving any money from the trafficker for the campaign.
The memo said the same trafficker bribed legislators after that election to ensure that President Hernández would be elected the president of the Honduran Congress. President Hernández later thanked the trafficker and told him he would be “protected from prosecution and law enforcement targeting,” prosecutors wrote.
In 2013, the trafficker spent $1.5 million to support President Hernández’s presidential campaign and an additional $40,000 to support his re-election in 2017, the memo said.
The memo does not name the trafficker but describes him as a cooperating witness, labeling him CW-3.
President Hernández has said that he believes the American authorities are being assisted by Alexander Ardón, the former mayor of the Honduran city El Paraíso, on the border with Guatemala. Mr. Ardón was indicted in Manhattan in January on cocaine-importation charges.
The Honduran president has proved to be adept at bending to Washington’s priorities, which have long focused on stemming drug trafficking through Central America.
As president of the National Congress, he succeeded in pushing through a constitutional reform in 2012 that allowed extradition to the United States. After winning the presidency in 2013, he began sending accused leaders of Honduran drug cartels to stand trial in the United States. He also accepted United States aid to train specialized units of the Honduran security forces to fight drug traffickers.
But the combined efforts appear to have had little impact: The State Department said this year that “there is no concrete information to suggest the overall volume of illicit drugs being trafficked through Honduras has decreased.”
The prosecution’s recent memo also says that in 2014, after President Hernández was elected, he told a cousin, a high-ranking Honduran national police officer, that he was considering eliminating extradition because he was “concerned that the United States would submit an extradition request” for his brother. The law remains in effect.
A separate federal court filing in Manhattan suggests that prosecutors and the D.E.A. had the Honduran president in their sights as early as 2013, when they asked a judge to permit access to email accounts of the president and his sister, Hilda, who later died in a helicopter crash.
As for Tony Hernández, prosecutors say that “he believed that he could operate with total impunity.” Indeed, they said, some of the cocaine he helped ship from Colombia bore a stamp with his initials, TH.