Evidence described in the article suggests that the Pentagon's main interest was in maintaining relations with a close military ally, rather than in overturning the coup. Though the battle over Honduras appeared to be fought along partisan lines, in the end it was the Obama administration's State Department that sabotaged efforts to have Zelaya restored to the presidency, as statements by former Secretary Clinton and other high-level officials admit.
Since the coup, the militarization of Honduras has increased. While human rights abuses continue to shock the public, US security assistance and military training continue unabated. Under President Trump and the coterie of military officers surrounding him, including former SOUTHCOM commander and now White House chief of staff John Kelly, US-backed militarization appears likely to deepen in Honduras and elsewhere throughout the region.
"What this reveals are behind-the-scenes aspects of an episode that profoundly damaged the US relationship with Latin America as a whole, as the US was an outlier in supporting the coup, and opposition to the coup among Latin American governments was led by Brazil," Johnston says. "In the end, the US State Department quietly allowed the military and other hard-line factions to determine policy and support the coup's success."
This story is especially relevant for the current moment, as the hard-line, military factions who prevailed in shaping the US response to the Honduran coup are now in senior positions in the Trump administration, raising troubling prospects for what the US reaction to another military coup d'etat would be under Trump.