Fort McNair, one of the oldest U.S. military posts in the country, is nestled on an outcropping of land where the Anacostia and Potomac rivers meet in Washington, D.C. There, within the National Defense University, is the Center for Hemispheric Defense Studies, where hundreds of Hondurans took courses over the years. In mid-July 2009, Honduran military officials sought the center’s help to solve a problem that had recently arisen. The Honduran military had just dispatched of its previous problem, President Manuel Zelaya, with a military coup. Now, the Central American military was facing international and regional condemnations for a brazen display of 1970s behavior in the 21st century. The military officials needed friends in the U.S. to rally behind it, but the Americans were wary of open shows of support. The U.S. had just revoked visas from top Honduran civilian and military officials, and suspended some security assistance. Two Honduran colonels were dispatched to Washington on a mission to convince the Americans that the Honduran military’s involvement in the coup was in fact constitutional. The military had reached out to the CHDS’s academic dean to get help for the delegation. Officially CHDS said no, Kenneth LaPlante, CHDS’s then-deputy director, told me. However, according to Martin Andersen, a former CHDS communications director who became a whistleblower, Gen. John Thompson, the academic dean, had allegedly provided “behind-the-scenes assistance in Washington, D.C., to Honduran coup plotters.” Andersen’s allegation was made in a complaint being investigated by the Department of Defense Inspector General, which has taken no action. At the time of the coup in Honduras, a number Republicans who supported the Honduran military sat on the American Security Council Foundation’s Congressional Advisory Board. One of the Republican representatives, Connie Mack, R-Fla., announced a “fact-finding” mission to Honduras while the colonels were in town. The Honduran colonels had a number of congressional meetings, which Andersen alleges Thompson helped facilitate. Thompson, who served on the foundation’s board in 2009, did not respond to a request for comment from The Intercept about his role. Cresencio Arcos, a former U.S. ambassador to Honduras who had taken a job at CHDS by the time the coup occurred, told me that he received an angry call from a congressional staffer who had met with the Honduran colonels. The colonels, Arcos said, had told the staffer they had CHDS’s support. He confronted CHDS’s director, Richard Downie, and his deputy, LaPlante, telling them, “We cannot have this sort of thing happening, where we’re supporting coups.” LaPlante denied ever being confronted about the allegations concerning CHDS or Thompson by anyone other than Andersen, the whistleblower, who raised the issue at the time. He said that since it was the allegation of just one individual, it was not seriously pursued. CHDS never officially provided any support or encouragement, LaPlante told me, but that “if it was CHDS or the Pentagon … yeah, personal opinions of professionals were shared.” That’s how the world works, he said. For Arcos, however, the implication of assistance for the Honduran military by any U.S. general are clear. “What are they going to conclude?” Arcos asked rhetorically. “That indeed there was complicity on the U.S. side.” Honduran politicians and businessmen who backed the coup were already hard at work lobbying in the halls of Congress – one group even set up an informal headquarters in a company’s conference room in downtown D.C., according to a former Honduran military officer who lives in the Washington area, who requested anonymity. While not a coordinated plan between the two parties, the support from a U.S. general likely buoyed their effort. A retired U.S. military intelligence officer, who helped with the lobbying and the Honduran colonels’ trip, told me on condition of anonymity that the coup supporters debated “how to manage the U.S.” One group, he said, decided to “start using the true and trusted method and say, ‘Here is the bogeyman, it’s communism.’ And who are their allies? The Republicans.” A network of former Cold Warriors and Republicans in Congress loudly encouraged Honduras’s de facto regime and criticized the newly elected Obama administration’s handling of the crisis. Zelaya, so his critics alleged, was simply an acolyte of Venezuelan President Hugo Chávez, public enemy No. 1 of the U.S. in the hemisphere. The U.S. had publicly worked for months to avoid the coup, and then to overturn it. But, on the ground in Honduras and behind closed doors in Washington, a parallel, personal diplomacy was leading U.S. policy down a very different path. New details of how the coup and its aftermath unfolded— based on unpublished government records and dozens of interviews with high-ranking U.S. and Honduran military officials, policymakers, and other key sources as part of an in-depth investigation by The Intercept and the Center for Economic and Policy Research — offer a glimpse into how the U.S. foreign policy apparatus dealt with the crisis. The new information paints a picture of an American government with no single policy, but rather, of bloated bureaucracies acting on competing interests. Hidden actors during the crisis tilted Honduras toward chaos, undermined official U.S. policy after the coup, and ushered in a new era of militarization that has left a trail of violence and repression in its wake.

Photo: Jose Cabezas/AFP/Getty Images

Early in the morning on Sunday, June 28, 2009, Honduran Special Forces escorted President Manuel Zelaya from his residence at gunpoint. Hours later, a dazed Zelaya appeared on the tarmac of the airport of San José in Costa Rica. He was still wearing his pajamas. Back in Honduras, the military cut off power across the country, blocking media from reporting on the unfolding coup d’état. For months, Zelaya had engaged the country’s elite-controlled institutions in a risky game of chicken over a non-binding referendum on reforming the country’s constitution. Honduras’s traditional power brokers saw the referendum as means for Zelaya to consolidate power at their expense and were prepared to go to great lengths to prevent it from happening. On June 25, Honduran legislators were prepared to vote in favor of deposing Zelaya, a power they did not have. Alerted to the machinations, U.S. Ambassador Hugo Llorens intervened, warning that the U.S. would oppose to the unconstitutional action. The Honduran legislators pulled back and the coup was put on hold — but not for long. By the next day, Zelaya’s powerful opponents were stepping up pressure on the Honduran military to act to prevent the referendum from taking place on June 28, as scheduled. A top adviser to the Honduran military high command told me that that evening they called the U.S. embassy in order to make clear that Zelaya should withdraw the referendum, “or we would be forced to act.” But this time, according to the Honduran military adviser, the warning was met with indifference. “The embassy was too naive,” the military adviser, who requested anonymity because they are still involved in Honduran political and military affairs, claimed. “They believe everything that their sources tell them.” Arcos, the former U.S. ambassador, agreed. He told me he spoke with Llorens the morning of Zelaya’s ouster. While Llorens had been working to avoid a coup, Arcos argued that the ambassador “gave [Hondurans] space because he thought some of his political interlocutors would prevail and stop these guys.” In the end, said Arcos, “he lost control.” Llorens did not respond to a request for comment. But, similar to the microcosm of the U.S. government, embassies are composed of representatives from an alphabet soup of agencies, each with their own contacts, interests, and chains of command.

Photo: Orlando Sierra/AFP/Getty Images

After the coup, the State Department told the press that U.S. officials had been “almost constantly engaged” to find a peaceful solution and had been in regular contact with the Honduran military. In fact, the two militaries were so close that the night before the coup, American military officers and diplomats were at a party at the U.S. defense attaché’s house, with their Honduran counterparts. The closeness was demonstrated in the timeline established by multiple interviews and an official record obtained through the Freedom of Information Act by independent researcher Jeremy Bigwood. At 9 p.m., while at the party, Col. Kenneth Rodriguez, the U.S. Military Group commander in Honduras, received an urgent call asking him to meet with the head of the Honduran military, Gen. Romeo Vásquez Velásquez. The Military Group, which operates outside the embassy’s chain of command, works directly with CHDS to oversee training programs and security assistance. Rodriguez agreed to meet, and later advised Vásquez and other top officers present to remain within the bounds of the constitution. There was no discussion of what was about to occur, according to the official record. At 10 p.m., Vásquez allegedly received a call asking him to come to the Supreme Court. Vásquez invited the American officer, who declined the offer and returned to the attaché’s party. The defense attaché was told of the meeting, but according to email records Bigwood obtained through FOIA, it wasn’t reported to the U.S. ambassador for 12 days. The attaché, Col. Andrew Papp, told me that when he heard about the meeting, it didn’t raise any concerns. He, as well as Rodriguez, insisted that the U.S. had no advanced knowledge of the coup. As early as June 26, however, according to recently obtained intelligence documents, Pentagon sources in Honduras believed it likely that Zelaya’s proposed referendum would “not happen” and that Zelaya “could be forced to resign” due to military opposition. The morning of Zelaya’s ouster, word of the military’s actions traveled quickly to Washington, and officials scrambled to respond. On June 28, the State Department and White House released statements that, while expressing concern, did not refer to the events in Honduras as a coup, instead simply calling for dialogue. Thomas Shannon, the State Department’s top official for the Western Hemisphere and a Bush administration holdover, emailed Secretary of State Hillary Clinton’s aides to inform her he was “working up press points.” Shannon’s position made him a main architect of the U.S. response. He did not reply to a request for comment. On June 29, however, President Barack Obama declared that “the coup was not legal,” and that Zelaya remained the legitimate president of Honduras. “It would be a terrible precedent if we start moving backwards into the era in which we are seeing military coups as a means of political transition rather than democratic elections,” Obama said. Days later, Rodriguez, the same official who met with the Honduran military leaders the eve of the coup, reported: “Most Hondurans I’ve talked to are confused by the U.S.’s reaction and feel somewhat abandoned by us.” Rodriguez told me that most Honduran officers knew the U.S. didn’t really like Zelaya, and they thought “it would be seen as politically expedient to get a new guy that is favorable to the U.S.” Col. Herberth Bayardo Inestroza, of the Honduran army, told the Miami Herald a few days after the coup that the military had broken the law in flying Zelaya out of the country, but then added, “It would be difficult for us, with our training, to have a relationship with a leftist government. That’s impossible.”

Honduran Chief of Joint Staff, Romeo Vasquez Velasquez (C), speaks to the press after overseeing the exit of ousted Honduran President Manuel Zelaya aboard the aircraft of Dominican President Leonel Fernandez in Tegucigalpa January 27, 2010. Photo: STR/AFP/Getty Images

Just after noon on June 28, 2009, Martin Andersen, the CHDS whistleblower, sent an email to Frank Mora, the Obama administration’s top defense official for the Western Hemisphere. Andersen understood the U.S. would be blamed for the coup by some in the hemisphere. In order to get out in front, he suggested “a brief be prepared of US — and particularly [Department of Defense] — relationships with Gen. Romeo Vásquez Velásquez and his closest aides.” The dossier would have stretched back decades. Vásquez completed courses in 1976 and again in 1984 at the School of the Americas in Fort Benning, Georgia, an institution that trained Latin American militaries attended by countless officers implicated in coups and human rights abuses in the region. This foreign military training system has helped perpetuate the militarization of the region. With little oversight, the disparate interests, ideologies, and personal relationships of those involved continue to carry at least as much weight as any official policy position announced from the State Department’s press room. In 2000, facing growing criticism to shut down the initiative, the School of the Americas temporarily closed. In 2001, it reopened as the Western Hemisphere Institute for Security Cooperation, and the George W. Bush administration appointed Richard Downie to run it. He was joined by Kenneth LaPlante. It was the same duo who would be running CHDS years later at the time of the Honduran coup. Together, with Thompson and other key staff, they formed a “clique” atop the center “who saw this as an opportunity to do what they goddamn well please,” James Zackrison, a former CHDS professor, told me in an interview. According to Zackrison, the center was effective at networking with militaries throughout the hemisphere, but not much else. The ex-Honduran military officer who now resides in the Washington area told me that his friends in the Honduran military “speak very highly” of Thompson. When the Honduran colonels came to Washington, they met with high-level State Department officials for breakfast at the historic Old Ebbitt Grill, a block from the White House. The colonels wanted to speak directly with the Pentagon, but State wanted their help first. Throughout July and August 2009, the U.S. brokered negotiations, ostensibly aimed at restoring Zelaya to the presidency and finding a diplomatic end to the crisis. The head of the Honduran congress, Roberto Micheletti, had been installed as president, giving the coup a civilian face, but the Honduran military appeared to be the only institution capable of changing the balance of power. A statement appeared on the Honduran Armed Forces’ website in late July pledging to respect any political solution that was reached, including Zelaya’s restoration. “That was our breakthrough,” said Fulton Armstrong, a former CIA analyst and staffer for Sen. John Kerry, D-Mass., at the time. It appeared this would remove the biggest obstacle to Zelaya’s restoration. But according to a source involved with the delegation, who requested anonymity, “the military didn’t want Zelaya back.” The colonels told the source, who had worked for days to facilitate the communique, to “forget it.” Negotiations continued to stall, and Armstrong’s hope for a breakthrough was quickly dashed. He’d soon have a better understanding of why. In August, army chief Gen. Miguel Angel García Padgett and other top Honduran military officials appeared on a popular Honduran TV program and defended their actions. Padgett said that he had discussed the dangers of socialism in the region at the CHDS in Washington and that the military’s actions should be praised as they prevented socialism from coming “to the borders of the United States.” Armstrong told me he met with CHDS’s leadership and asked for an explanation. CHDS’s mandate was ostensibly to instill the value of civilian control over the military, and yet the coup was being justified by “a military that’s citing you for support for overthrowing a government,” Armstrong recalled telling CHDS officials then. Armstrong believes that CHDS’s comments encouraged the Honduran military and its de facto government not to accept any negotiated settlement. An academic named Jonathan Caverley, an associate professor at the Naval War College, co-authored a 2015 working paper that linked foreign military training with an increased likelihood of military coups. “It’s not that they” — coup leaders — “think the U.S. will support them because they went to the War College,” he told me. “It’s more like, ‘I have this relationship and these skills, I can make this easier.’” Days after Padgett appeared on TV, CHDS was already looking to establish new relationships in Honduras. Downie wrote to Llorens, the U.S ambassador, asking if he had recommendations for students to come to CHDS. The letter, obtained through FOIA, contains a scribbled personal note in the margin from Downie: “This may be hard now. But, hope soon this will be a useful opportunity to strengthen relations w/ key counterparts when the situation changes.” A top State Department official, who was involved in Honduras policy at the time and requested anonymity, told me that he was aware of the actions that some individuals took to support the coup, but that what happened at CHDS “was not what the Pentagon was doing.”

Photo: U.S. Southern Command

Staff at CHDS were in regular communication after the coup with their colleagues at the Pentagon’s Latin American subsidiary, the U.S. Southern Command, known as SOUTHCOM, according to email records I obtained through FOIA. Stephen Meyer, a retired military officer, served as a liaison between CHDS and SOUTHCOM. Years earlier, he was the U.S. Military Group commander in Honduras when Arcos served as ambassador. Meyer reported directly to Thompson, according to a job description posted online. On June 30, CHDS director Downie sent a document to top Department of Defense and State Department officials with the subject line “Honduras Situation: CHDS Perspective on Scenarios and Implications for Way Ahead.” The copy of that email obtained through FOIA is redacted in its entirety. But, in an interview, LaPlante, the former CHDS deputy director, said the basic analysis was that the U.S. wouldn’t want to push Zelaya back into office and so it would give the coup government some time to set things up before moving on to elections. It wasn’t the official line of the U.S., but “that’s what ended up happening,” he said. The U.S. simply had too many vested interests to take any other position. The arc of Arcos’s career — he was a Foreign Service officer in Honduras at the height of the Cold War before becoming ambassador — speaks to these American investments in Latin America. In the early 1980s, Arcos was part of a team that helped ensure U.S. military access to Soto Cano, a Honduran base 50 miles outside the capital, Tegucigalpa, to create a staging ground for U.S. support for Central American military regimes and right-wing insurgencies, most notably the Contras in neighboring Nicaragua. When SOUTHCOM’s mission moved from fighting communism to the War on Drugs, Soto Cano only became more important. In the 1990s, SOUTHCOM’s budget increased more than any other U.S. military regional command. As other bases closed, Soto Cano became “the only game in town,” said Arcos. In the years preceding the coup, Zelaya increasingly spoke of using the base as a commercial airport. In June 2008, in response to Zelaya’s plans, then-U.S. Ambassador Charles Ford wrote that the U.S. would keep a “low public profile” while working to “protect U.S. security interests at Soto Cano.” When Ford left the embassy, he took a job with SOUTHCOM. The morning of the coup, before soldiers flew Zelaya to Costa Rica, they brought him to Soto Cano. Some 600 American soldiers were stationed at the base in 2009, and American officers shared responsibility for the control tower with their Honduran counterparts. Zelaya was transferred to the bright blue presidential plane. The U.S. has always maintained that it had no knowledge of the plane’s passengers that morning.

Photo: Ginnette Riquelme/AP

Enrique Reina, Zelaya’s private secretary at the time, told me he called the U.S. ambassador early the morning of the coup before Zelaya was taken into exile. Llorens told him he would try to intervene and stop the plane from departing, Reina said. It left anyway. “The Honduran military doesn’t do anything without the U.S. approving it,” Reina remarked. A few hours later, at 10 a.m, Tom Shannon, the State Department official working on Western Hemisphere issues, emailed top officials in Foggy Bottom. Shannon wrote that he was reaching out to SOUTHCOM to ensure a coordinated response. “We have big military equities in Honduras,” he wrote. The U.S. announced on July 1 that it had “cut off contact with those who have conducted the coup.” On the ground, however, that restriction was secretly lifted the next day. Clinton, the then-secretary of state, wrote to the embassy on July 2 giving approval to “engage elements of the Honduran Armed Forces and de facto regime,” according to a diplomatic cable obtained through Bigwood’s FOIA, which has never been publicly revealed. The telegram instructed the ambassador to use the approved contact to “explore options for Zelaya’s peaceful resumption of his office.” Clinton went on, “You shall avoid giving the appearance that we are extending official recognition or acceptance of Micheletti and his colleagues and their actions.” Enforcing the ban would have been difficult anyway, given the close personal relationships at hand. When I contacted Rodriguez, the American officer who met with top Honduran military leaders on the eve of the coup, he told me that he “loved” Vásquez and his wife, whom he had gotten to know quite well over his stint in Honduras. It’s not unusual for military officials and their families to become close friends with local officers; they dine at the same restaurants, shop at the same malls, and have one another’s cellphone numbers. Papp, who had hosted the party the night before the coup, said he and his officers became the primary conduit for most communications. They were the ones with the contacts. Rodriguez told me his Honduran military counterparts wanted him to acknowledge that the pressure from the Obama administration and State Department would relent. He recalled that they wanted to hear him say, “The administration is saying one thing, but the military says otherwise.” However, he claimed to support the administration policy, and said that’s what he told his friends. But according to Papp, the message he delivered to the Hondurans was that “we still wanted a relationship when this was all done with.” Publicly, the State Department said the coup government would eventually recognize how isolated it was and would relinquish power, but the Pentagon sent a contradictory message: the two countries could get through the crisis together, regardless of the situation on the ground. For Papp, his concern as a senior military official was that the Honduran military “is very friendly with the U.S.” — and that the U.S. needed to protect its interests, including the largest military base in the region, which was in Honduras. Pentagon officials, however, were not only seeking to influence U.S. policy through their on-the-ground contacts in Honduras. After the coup, a multiagency committee to oversee U.S.-Honduras policy was set up in Washington. “If you ask they question, ‘Who’d have the most heavyweight presence at the [committee]?’ — it’s clearly the Department of Defense,” Arcos said. Despite internal and public pressure to take a harder line against the Honduran military, the State Department formally determined that Zelaya’s ouster was not a “military” coup in early September. The U.S. response “came out more measured than it could have,” Papp told me. “And I think that’s a good thing.” Papp claimed the U.S. did what it could to support Zelaya, but the real issue “was we didn’t really like the guy.” Putting off any potential stronger response until elections in November 2009 ended up being a pretty good option, he told me. As early as July, however, SOUTHCOM had assessed that the coup government could prevail in elections merely by holding out until ballots were cast, according to U.S. military intelligence documents obtained through Bigwood’s FOIA request. “To defeat Zelaya, the de facto government needs only to endure until new elections occur,” the documents said. The coup government — encouraged by individuals within the U.S.’s sprawling foreign policy bureaucracy — did hang on. But for elections to serve as a way out of the crisis, it would take a change in the U.S. government’s official policy. The U.S. would have to recognize elections held under the coup regime in an increasingly repressive atmosphere, and against the wishes of the rest of the hemisphere.

Gen. Romeo Vasquez, center left, head of the Joint Chiefs of Staff fired by Honduras’ President Manuel Zelaya late Wednesday for refusing to support a referendum, is greeted by demonstrators during a protest in Tegucigalpa, Friday, June 26, 2009. Photo: Esteban Felix/AP

On the surface, the battle over Honduras in Washington appeared to be fought along partisan lines. The reality was that key actors on both sides were working toward the same goal: elections without Zelaya’s prior restoration to office. In July, Sen. Jim DeMint, R-S.C., the loudest Republican critic of the Obama administration’s Honduras policy, put a hold on the confirmations of two top State Department officials, Arturo Valenzuela and Shannon. Valenzuela, nominated to replace Shannon as the top official for the Western Hemisphere, had called the situation in Honduras a “classic military coup” at his confirmation hearing. Shannon, meanwhile, had been tapped to become U.S. ambassador to Brazil. DeMint’s move was a throwback to the Cold War, when cheerleaders for foreign right-wing militaries in the Senate blocked nominations as a means of influencing U.S. foreign policy. The hold on Shannon’s appointment also meant that one of the people most responsible for U.S. policy after the coup was now fighting for his career. “He was caught,” Arcos told me. Zelaya was perceived as a “Chávez guy,” Arcos said, and working to restore him to office, as the administration claimed was its objective, would have been career suicide for Shannon. Immediately after the coup, the State Department “strategized on a plan to restore order in Honduras and ensure that free and fair elections could be held quickly and legitimately, which would render the question of Zelaya moot,” Clinton wrote in her 2014 memoir, “Hard Choices.” It was a stunning admission from the former secretary of state. Holding out until the elections was the coup supporters’ game plan and exactly what Republicans like DeMint were calling for. Some Democrats pushed back against DeMint and the Clinton State Department, including House Foreign Affairs Committee Chair Howard Berman, D-Calif., who urged Clinton to “call it a coup.” The pressure to take a tougher line on the coup, however, became too much for the State Department to bear. It announced in early September that it wouldn’t simply wait out the vote, and the U.S. “would not be able to support the outcome of the scheduled elections.” The U.S statement, though, made no explicit mention of what the rest of the hemisphere had called for in an August resolution of the Rio Group, comprised of every Latin American and Caribbean government: that Zelaya’s restoration be a precondition for recognizing elections. (U.S. officials went as far as to block a similar resolution that was introduced in the Organization of American States.) “The wording is deliberately vague,” wrote the U.S. embassy’s economic counselor a week later, in an email I obtained. “This has to be about restoring democratic, constitutional order in Honduras, not just restoring Zelaya.” The diplomatic official went on, “We need to be looking to the future and to making Honduran democracy stronger as a result of all this. Making this solely an issue of Micheletti and Zelaya does not accomplish that goal. They should both be irrelevant after November 29.” The statement was meant to “cut the legs out from under” Venezuela and its allies, who insisted upon Zelaya’s return to the presidency, according to the economic counselor’s email. The foreign policy machine had bought into the analysis of its biggest critics. In mid-September, Shannon met with Micheletti, the head of the post-coup government, and told him, “The U.S. wanted to find a way to support the Honduran elections, but that a negotiated agreement was necessary,” according to a diplomatic cable released by WikiLeaks. With Zelaya’s negotiating team, Shannon was very clear that the U.S. would ensure Zelaya’s restoration was part of any agreement, according to multiple sources. In October, however, Shannon met with DeMint and his top foreign policy staffer at the time, Chris Socha. Shannon “said very, very clearly” that the U.S. would recognize the upcoming elections regardless of Zelaya’s restoration, Socha claimed. At the end of October, a deal was finally reached between the two sides in Honduras, but it contained a loophole: The Honduran congress would vote on restoring Zelaya to office. Days later, Shannon delivered the final blow. On November 3, during a live TV interview, he stated publicly what he had allegedly already agreed to in private: The U.S. would recognize the election regardless of Zelaya’s status. The deal that had taken so long to put together was dead. DeMint lifted his hold on Shannon’s nomination as ambassador to Brazil within days. International election observers, as well as many Honduran candidates, boycotted the election. The U.S. bucked the trend, funding its own observers and then recognizing the results, thereby souring relations with the hemisphere. With the election, the coup’s legacy was ensured and those surprised by the initial U.S. condemnation were vindicated.

Honduran President Juan Orlando Hernandez addresses supporters following victory in the primary elections of the National Party in Tegucigalpa, March 12, 2017. Photo: STR/AFP/Getty Images