Research support for this article was provided by the Puffin Foundation Investigative Fund at The Nation Institute.

News travels fast across the red desert bush of remote Djibouti. Even as US military reservists erect a field hospital around a cluster of tents and blockhouses near a desolate watering hole, dozens of tribespeople are waiting for treatment in orderly rows. They arrive with maladies of every sort: bad teeth, diarrhea, fevers, colds, arthritis. At the triage center, an elderly tribesman has had a thorn removed from his foot, a wound that had been infected for months. At the dental surgery station, Navy Lt. Bill Anderson, an orthodontist from Northfield, New Jersey, will over the next few hours extract a dozen rotting or impacted teeth using instruments that sparkle in the late-morning sun.

The reservists are attached to a Djibouti-based task force of some 1,800 soldiers, marines, sailors and Air Force personnel. Embedded with them is an aid specialist from the Agency for International Development, which provides guidance for the operation. She is reticent and refers questions to the agency’s country leader, Stephanie Funk. The next day, Funk acknowledges that USAID’s solitary representation on the triage mission is symptomatic of a new age in US foreign policy–one in which America, in peacetime as much as in war, is personified abroad more by soldiers than by civilians. “If we had the numbers and the money to do fieldwork, we would, but our budgets have been declining for years,” Funk said in her office on the US Embassy compound in Djibouti City. “The Pentagon has got both numbers and money. For every fifty of them, there’s only one of me.”

Quietly, gradually–and inevitably, given the weight of its colossal budget and imperial writ–the Pentagon has all but eclipsed the State Department at the center of US foreign policy-making. The process began with the dawn of America’s post-World War II global empire and deepened in the mid-1980s, with the expansion of worldwide combatant commands. It matured during the Clinton years, with the military’s migration into humanitarian aid and disaster relief work, and accelerated rapidly with George W. Bush’s declaration of endless conflict in the “global war on terror” and a near-doubling of military spending.

In addition to new weapons and war fighters, the Pentagon’s budget now underwrites a cluster of special funds from which it can train and equip foreign armies–often in the service of repressive regimes–as well as engage in aid development projects in pursuit of its own tactical ends. Although these programs must be conducted with State Department approval and are subject to Congressional review, legislative oversight and interagency coordination is spotty at best. The Pentagon, meanwhile, is pushing for full discretionary control over these funds–a move that would render meaningless the 1961 Foreign Assistance Act, which concentrated responsibility for civilian and military aid programs within the State Department.

Defense Secretary Robert Gates has lamented the resource gap between civilian and military agencies, most pointedly in a July 2008 speech, when he warned of the “creeping militarization” of foreign policy. He has wryly pointed out how, given the Defense Department’s $664 billion budget compared with the State Department’s $52 billion annual outlay, Washington employs more military band members than it does foreign service officers. No one at the Pentagon, however, is calling for the restoration of State Department primacy over foreign affairs and a proper budget to finance it. Rather, Defense officials speak of a civilian-military “partnership” in which, some fear, an underfunded State Department would be reduced to a mere subcontractor for Pentagon initiatives.

Secretary of State Hillary Clinton has suggested she will re-establish the State Department as the fountainhead of foreign policy. But she has said little about the Pentagon’s expanded funding authority, and her embrace of what she calls “the three Ds” of her mission–defense, diplomacy and development–implies DoD’s preoccupations are in concert with her own. Nor has she suggested she might allow greater autonomy for USAID, where officials grumble about how their work is as routinely politicized by the State Department as it is by the Pentagon. Indeed, Clinton has yet to name a new permanent director.

Though Clinton has presided over a marked increase in USAID’s budget, diplomats and politicians say an overhaul is way overdue. “Without a more robust aid agency,” Richard Lugar, the ranking minority member on the Senate Foreign Relations Committee, wrote in the August 9 Washington Post, “President Obama’s pledge to double foreign assistance would be like adding a third story to a house that had a crumbling foundation.” Lugar, along with Senator John Kerry, is promoting a bill that would give USAID the lead role in coordinating foreign assistance.

The Pentagon, meanwhile, is flexing its own policy-making muscle. As Bush’s wars grew in scope, so too did the military’s aid budget and its focus on nonlethal activities–what DoD once referred to as “military operations other than war.” Now known by the conveniently vague and expansive handle of “stability operations,” and funded by a war chest passed into law three years ago, these missions are often deeply at odds with the goals of diplomats and civilian aid workers. Perversely, the Pentagon is militarizing foreign policy even as it “civilianizes” the character of its activities abroad.

Civilians figure at least as heavily as generals and admirals in the pantheon of American militarism. It was George W. Bush and Donald Rumsfeld–with the collusion of Condoleezza Rice–who expanded and entrenched the Pentagon’s franchise over foreign policy. Rumsfeld’s contempt for civilian authority was demonstrated most clearly, and with devastating results, in the run-up to the war in Iraq. Aside from bulldozing the constitutional prerogatives of Secretary of State Colin Powell, he vigorously, if stealthily, subverted the nation’s civilian leaders abroad. Before the US invasion, for example, he dispatched a three-man team to gather intelligence in several Middle Eastern states without informing the ambassadors of their activities, according to a source with intimate knowledge of the episode. The secret deployment has been widely interpreted as a direct violation of the executive Letter of Instruction to Chiefs of Mission, first signed by President Kennedy, which gave the US ambassador in his host country “full responsibility for the direction, coordination, and supervision of all Department of Defense personnel on official duty.”

Rumsfeld also blocked NGOs from any substantial role in postwar Iraq, soft-stalling their efforts to obtain licenses to enter pre-invasion Iraq and stonewalling their requests for information on procedures once Saddam Hussein’s regime had been destroyed. “The plans were classified,” Sandra Mitchell, then a vice president for the International Rescue Committee (IRC), said in an interview at the time. “We would get answers like, ‘We’re working on it. Don’t worry. We’ll be handling this.'”

The results were calamitous, and since then the Defense Department has aggressively sought the support and expertise of civilian aid groups–so much so that InterAction, a coalition of American NGOs, was compelled to issue a code of conduct to its members to lessen the chances for blowback, which often comes from working with the military. “To the extent that we become identified with the US military, we become compromised,” says George Rupp, president and CEO of the IRC. “We’re trying to keep it from changing the way we do business, but things may be changing whether we like it or not.”

Despite the Foreign Assistance Act’s stipulation of State Department authority, the Pentagon accounts for nearly a quarter of America’s budget for overseas direct assistance–up from near zero a decade ago–while USAID’s share has declined to 40 percent from 65 percent during the same period. Moreover, as the Pentagon’s funding capacity has expanded, so has its foray into humanitarian aid and social development. Directive 3000.5, a November 2005 Pentagon mission statement, defines stability operations as “a core U.S. military mission” to be conducted “across the spectrum from peace to conflict, to establish or maintain order in States and regions.” It tasks US forces to develop, among other things, “a viable market economy, rule of law, democratic institutions, and a robust civil society,” including “various types of security forces, correctional facilities, and judicial systems.”

Any mission conducted “from peace to conflict…in States and regions” is by definition everlasting and all-encompassing, and Directive 3000.5 chills the foreign aid and diplomatic community. The document concedes that humanitarian and development work is often best performed by civilian experts, and it encourages their input. But it also makes clear that “US military forces shall be prepared to perform all tasks necessary to establish or maintain order when civilians cannot do so.”

The Pentagon says it needs its own aid budget because assistance programs run by the State Department are overly bureaucratic. It argues that aid developed and administered directly by the Defense Department, such as the Pentagon’s recent appeal for $400 million in emergency funding to train and equip the Pakistani army, will be more responsive and yield faster results. Critics respond that such a narrow focus on military concerns will crowd out other foreign policy priorities like the promotion of human rights, education and healthcare. “If DoD is concerned that civilian-led processes are too slow, then let’s talk about how we fix those processes,” says Gregory Elias Adams of Oxfam America. “Let’s have a conversation about how the interagency process is broken and needs to be fixed. If civilian agencies do not have capacity to contribute to the mission, it will be military imperatives that carry the day.”

In the January/February issue of Foreign Affairs, former ambassador J. Anthony Holmes noted how in June 2008 the State Department had only 10 percent more diplomats and support staff than it had a quarter-century ago, when there were twenty-four fewer countries in the world and US interests were concentrated in Europe and Northeast Asia. Unlike the military, which bases a fifth of its 1.6 million active-duty servicepeople overseas, the diplomatic corps posts nearly three-quarters of its people abroad. As a result, Holmes argues, the State Department lacks “surge capacity,” the ability to train and retrain personnel or rotate them to hot spots without having to leave their posts empty in the interim.

Absent a far more aggressive restructuring of civilian aid and diplomatic agencies, their dependence on the military will only intensify. In April the White House backed away from a pledge to staff hundreds of posts in Afghanistan with civilians for lack of funding and said it would instead turn to the Pentagon. Meanwhile, efforts to set up an expeditionary corps of some 2,500 civilians under State Department leadership have snagged on interagency snits, Congressional lethargy and funding constraints.

The Obama administration has acknowledged the problem. In its budget for 2010, it calls for 1,300 new foreign service officers, and it is planning a near doubling of the State Department’s foreign aid budget from 2008 levels–a step in the right direction, say aid workers and diplomats, but not nearly enough to meet the department’s commitments. “I have never seen a better opportunity to rebalance the tool kit,” says Gordon Adams, a Clinton administration national security expert and now a professor at the American University’s School of International Service. “But there remains a serious discontinuity between the structure of Defense and the structure at State. One of the many questions [Secretary of State] Clinton will have to answer is how to deal with the military on a regional basis overseas.”

It is overseas, after all, where US foreign policy is implemented, and it is there that the State Department’s authority is so plainly obscured by the Pentagon’s shadow. As part of a broader effort to reform the Defense Department’s chain of command, the world was divided into operational zones in 1986. The centrality of these regional commands and the men who lead them–the best-known is Gen. David Petraeus, head of Central Command, or Centcom, which is responsible for US security efforts from the Persian Gulf to Central Asia–has increased as the Pentagon endows them with ever larger missions and budgets. In particular, the combatant commander has the authority to fund military cooperation agreements with governments in his area of responsibility, a mandate that was once concentrated within the Office of the Secretary of Defense. That prerogative alone gives the commanders enormous prestige with host governments at a time when their civilian counterparts, from ambassadors on down, have been pauperized by spending cuts that date back to Senator Jesse Helms’s war on foreign aid in the 1990s.

In general, ambassadors and combatant commanders find common ground on many issues. But tensions, particularly in time of war, are inevitable. In 2003 then-Centcom commander Gen. John Abizaid wanted to build a $99 million counterterrorism facility in Jordan at the request of Jordanian King Abdullah II. The project was opposed as a needless extravagance by Edward Gnehm, US Ambassador to Jordan at the time. So Abizaid went around Gnehm by funding the training facility from his own budget, according to a source with intimate knowledge of the matter. (An e-mailed request to Abizaid’s office for comment was not returned.) The New York Times reported on March 8, 2006, that for about two years the Pentagon had been dispatching Military Liaison Elements–special operations teams tasked with gathering intelligence on suspected terrorists and ways to destroy them–to various countries without the US ambassadors’ knowledge. In Niger two years ago, the US chief of mission cut back the number of entry visas for US military personnel because of the country’s political fragility and because the embassy lacked the resources to accommodate them, according to a report by the Government Accountability Office.

If Command Strategy 2016 is anything to go by, however, the Pentagon has no intention of waiting around. Issued in March 2007, it describes Southern Command, or Southcom, which has responsibility for Latin America and the Caribbean, as a Joint Interagency Security Command that would “provide enabling capabilities to focus and integrate interagency-wide efforts to address the full range of regional capabilities.” As Adm. James Stavridis, then-leader of Southcom, elaborated at the time, “We want to be like a big Velcro cube that these other agencies can hook to so we can collectively do what needs to be done in this region.”

Needless to say, many of those “other agencies” are reluctant to go along for the ride, particularly given the US military’s checkered history in Latin America, where the Pentagon first began working independently with foreign governments. In 1988 lawmakers passed a bill ordering the military to arrest the flow of narcotics into the United States from Mexico, intensifying the failed “war on drugs” and lending thrust to the Pentagon’s neo-imperialist lunge into Latin America. “Southern Command should not be the coordinating agency, because then they become the face of US assistance in foreign regions,” says George Withers, a senior fellow at the Washington Office on Latin America. “The agency that coordinates controls the agenda.”

When he was chair of the Foreign Relations Committee, Senator Lugar dispatched aides around the world to quantify the effects of DoD’s expanded presence overseas and its growing dominance of US security policy. The result was two reports–committee “prints,” in Capitol Hill parlance–that provide an alarming account of how much of foreign policy has been ingested by the military. “As a result of inadequate funding for civilian programs,” concludes the first of the two prints, released in December 2006, “US defense agencies are increasingly being granted authority and funding to fill perceived gaps. Such bleeding of civilian responsibilities overseas from civilian to military agencies risks weakening the Secretary of State’s primacy in setting the agenda for US relations.”

The report disparages the 12-to-1 spending ratio between the Pentagon and the State Department, which it says “risks the further encroachment of the military, by default, into areas where civilian leadership is more appropriate because it does not create resistance overseas and is more experienced.” Left unchecked, it warns, the increase in the number of military personnel and Pentagon activities abroad could lead to “blurred lines of authority between the State Department and the Defense Department [and] interagency turf wars that undermine the effectiveness of the overall US effort against terrorism.”

The report contains many examples of the need for civilian authority “to temper Defense Department enthusiasm.” It cites an unnamed African country–“unstable, desperately poor, and run by a repressive government”–that appealed to the US military for help in fighting an insurgency. The Pentagon agreed and soon afterward hailed the nation as a “model country for security assistance.” Civilian embassy officials, however, expressed concern at the proliferation of US military personnel there. “It would be a major setback,” the print notes, “if the United States were to be implicated in support of operations shoring up the repressive regime, regardless of the stated intent of such training.”

The wellspring for such operations is Section 1206 of the 2006 National Defense Authorization Act, which allocated the Pentagon $200 million to spend on lethal and nonlethal equipment, supplies and training to foreign militaries. Section 1206 remains a limited authority, though last year legislators extended its budgeting cycle to three years, added maritime security to its list of activities and topped up its allocation to $350 million. A key condition Congress laid down for 1206 approval–that the Pentagon submit its programs list to the State Department for “concurrence” or “dual-key” approval–remains. Despite this, 1206 funds have been invested in countries with highly autocratic governments.

The US government has a long history of bankrolling dictators in pursuit of strategic ends. But there is a difference between declaring such support as official policy–as is the case with Egypt, for example–and the Pentagon’s dole, which Congress allots with only a perfunctory understanding of how the money will be spent. In August 2008 Senator Russell Feingold responded to the Pentagon’s request for additional 1206 funding with a report that $6 million from the program had been given to the government of Chad, which according to the State Department is “engaging in extra-judicial killing, arbitrary detention and torture.” Other recipients of 1206 funding are Algeria, Cameroon, Equatorial Guinea, Gabon and Tunisia, all of which have abysmal human rights records.

Conspicuously absent from the debate over Section 1206 was Condoleezza Rice. At the time, Senator Patrick Leahy wrote Rice several letters imploring her not to cede unprecedented power to the Pentagon. According to Paul Clayman, an attorney who has worked for the State Department as well as the Senate Foreign Relations Committee, and others who were closely involved in the debate, the staff on Lugar’s committee were staggered by Rice’s passivity.

In April 2008 Rice and Gates testified jointly before the House Armed Services Committee. In addition to their mutual desire for augmentation of the Pentagon’s Section 1206 channel, Rice also endorsed a new Pentagon-controlled allocation under Section 1207 of the defense bill that could fund State Department projects contingent on the defense secretary’s approval. At one point, Rice was asked by Congressman Vic Snyder whether she still believed ambassadors should be the most senior representatives of US missions overseas. Naturally, Rice answered in the affirmative. What was striking was the fact that the question had to be asked in the first place.

Congress is now pushing back–sort of. In its version of the Pentagon’s most recent supplemental budget, lawmakers stipulated that authority over the Pakistan counterinsurgency fund should reside with the State Department at the end of fiscal 2010. The House version of the bill called for State to assume immediate control of the fund, but the Senate prevailed in delaying the transfer, noting the department’s “lack of capacity.”

On the other hand, the House also appears to be leaning toward DoD in the 1206 debate. In a June report on the National Defense Authorization Act for fiscal year 2010, the House Armed Services Committee soft-pedaled its earlier position that 1206 programs should be transferred to State. Instead, it committed itself to the existing “dual key” framework and averred that “whatever the final, permanent form these authorities take, the Secretary of Defense must play a primary role in generating requirements.” The report also asserts that “the Department of State still lacks the capacity to execute these authorities.”

The Pentagon shows little inclination to relinquish its authority. An internal DoD memo issued last November characterized civilian agencies as too weak to help in counterinsurgency operations and declared that the Pentagon should be ready to lead such missions absent a “whole-of-government” approach. The document, leaked in January, warned that it would take civilian agencies at least a decade to develop the capacity to work effectively alongside the military. In February an unnamed “senior Pentagon official” told Inside the Pentagon, a weekly newsletter, that the military needed “a great deal of budgetary flexibility” in order to “proactively get ahead of problems before they become disasters.” In May, Michael Vickers, soon to become assistant secretary of defense for special operations, told Congress it should increase spending “several fold” for funding under Section 1208, a budget mandate exclusive to the Pentagon in support of “foreign forces, irregular forces, [and] groups or individuals” engaged in combating terrorism. The oversight mechanism for 1208 programs is considerably less rigorous than those associated with 1206.

Civilian Washington, in other words, has reaped its own whirlwind. It was not a military cabal but a civilian cadre–Clinton in the 1990s, followed by Bush and his neoconservative courtiers–who expanded the reach and lethality of the military, despite the collapse of the Soviet Union. As the executioner of foreign policy, so much of which is now imposed from the business end of a Predator drone, why shouldn’t the Pentagon serve also as its judge and jury? The answer, of course, is that America is a republic, a nation not of men but of laws, and the laws say foreign policy must be charted by civilians. Complacent politicians have neglected this trust, however, and the military now defines US interests abroad as much as it defends them. That is the bill for a leviathan. It is the wages of empire.