Hillary Clinton’s “regime change” policies as Secretary of State helped spread the chaos that has turned the Middle East into a killing field and might have done even worse if not for extraordinary obstructions from the Pentagon’s Joint Chiefs of Staff regarding Syria, as Gareth Porter recounts at Middle East Eye.

By Gareth Porter

Seymour Hersh’s recent revelations about an effort by the U.S. military leadership in 2013 to bolster the Syrian army against jihadist forces in Syria shed important new light on the internal bureaucratic politics surrounding regime change in U.S. Middle East policy. Hersh’s account makes it clear that the Obama administration’s policy of regime change in both Libya and Syria provoked pushback from the Joint Chiefs of Staff (JCS).

That account and another report on a similar episode in 2011 suggest that the U.S. military has a range of means by which it can oppose administration policies that it regards as unacceptable. But it also shows that the military leadership failed to alter the course of U.S. policy, and raises the question whether it was willing to use all the means available to stop the funneling of arms to al-Nusra Front and other extremist groups in Syria.

Hersh details a JCS initiative in the summer of 2013 to share intelligence on Islamic State and al-Qaeda organizations with other German, Russian and Israeli militaries, in the belief that the information would find its way to the Syrian army. Hersh reports that the military leadership did not inform the White House and the State Department about the “military to military” intelligence sharing on the jihadist forces in Syria, reflecting the hardball bureaucratic politics practiced within the national security institutions.

The 2013 initiative, approved by JCS chairman, General Martin Dempsey, was not the first active effort by the U.S. military to mitigate Obama administration regime change policies. In 2011, the JCS had been strongly opposed to the effort to depose the Muammar Gaddafi regime in Libya, a regime-change effort led by then-Secretary of State Hillary Clinton.

When the Obama administration began its effort to overthrow Gaddafi, it did not call publicly for regime change and instead asserted that it was merely seeking to avert mass killings that administration officials had suggested might approach genocidal levels. But the Defense Intelligence Agency (DIA), which had been given the lead role in assessing the situation in Libya, found no evidence to support such fears and concluded that it was based on nothing more than “speculative arguments.”

The JCS warned that overthrowing the Gaddafi regime would serve no U.S. security interest, but would instead open the way for forces aligned with al-Qaeda to take over the country. After the Obama administration went ahead with a NATO air assault against the Gaddafi regime the U.S. military sought to head off the destruction of the entire Libyan government.

General Carter Ham, the commander of AFRICOM, the U.S. regional command for Africa, gave the State Department a proposal for a ceasefire to which Gaddafi had agreed. It would have resulted in Gaddafi’s resignation but retain the Libyan military’s capacity to hold off jihadist forces and rescind the sanctions against Gaddafi’s family.

But the State Department refused any negotiation with Gaddafi on the proposal. Immediately after hearing that Gaddafi had been captured by rebel forces and killed, Clinton famously joked in a television interview, “We came, we saw, he died” and laughed.

By then the administration was already embarked on yet another regime change policy in Syria. Although Clinton led the public advocacy of the policy, then CIA Director David Petraeus, who had taken over the agency in early September 2011, was a major ally. He immediately began working on a major covert operation to arm rebel forces in Syria.

The CIA operation used ostensibly independent companies in Libya to ship arms from Libyan government warehouses to Syria and southern Turkey. These were then distributed in consultation with the United States through networks run by Turkey, Qatar and Saudi Arabia. The plan went into operation within days of Gaddafi’s death on October 20, 2011, just before NATO officially ended its operation at the end of that month, as the DIA later reported to the JCS.

But the result of the operation was to accelerate the dominance of al-Qaeda and their Islamist allies. The Turks, Qataris and Saudis were funneling arms to al-Qaeda’s Syrian franchise, al-Nusra Front, or other closely related extremist groups. That should not have surprised the Obama administration. The same thing had happened in Libya in spring 2011 after the Obama administration had endorsed a Qatari plan to send arms to Libyan rebels. The White House had quickly learned that the Qataris had sent the arms to the most extremist elements in the Libyan opposition.

The original Petraeus covert operation ended with the torching of the U.S. consulate in Benghazi in September 2012 in which Ambassador Christopher Stevens was killed. It was superseded by a new program under which Qatar and Saudi Arabia financed the transfer of weapons from other sources that were supposed to be distributed in cooperation with CIA officials at a base in southern Turkey.

But “thousands of tons of weapons” were still going to groups fighting alongside the jihadists or who actually joined them as Vice President Joe Biden revealed in 2014.

By spring 2013, al-Nusra Front and its Islamic extremist allies were already in control of wide areas in the north and in the Damascus suburbs. The Islamic State had separated from al-Nusra Front and established its own territory south of the Turkish border. The secular armed opposition had ceased to exist as a significant force.

The “Free Syrian Army”, the nominal command of those forces, was actually a fiction within Syria, as was reported by specialists on the Syrian conflict . But despite the absence of a real “moderate opposition,” the Obama administration continued to support the flood of arms to the forces fighting to overthrow Assad.

In mid-2013, as Hersh recounts, the DIA issued an intelligence assessment warning that the administration’s regime change policy might well result in a repeat of what was already happening in Libya: chaos and jihadist domination. The JCS also pulled off a clever maneuver to ensure that the jihadists and their allies were getting only obsolete weapons. A JCS representative convinced the CIA to obtain much cheaper arms from Turkish stocks controlled by officials sympathetic to the CIA’s viewpoint on Syria.

But the JCS failed to alter the administration’s policy of continuing to support the flow of arms into Syria. Did the military leadership really use all of its leverage to oppose the policy?

In 2013, some officials on the U.S. National Security Council staff pushed for a relatively modest form of pressure on Qatar to get it to back off its continued supply of arms to extremists, including al-Nusra Front, by pulling out a U.S. fighter squadron from the U.S. air base at al-Udeid in Qatar. But as the Wall Street Journal reported earlier this year , the Pentagon, obviously reflecting the JCS position, vetoed the proposal, arguing that the forward headquarters of the Central Command at the airbase was “vital” to U.S. operations in the Middle East.

The political implications of the episode are clear: bureaucratic self-interest trumped the military’s conviction that U.S. security is being endangered. No matter how strongly the JCS may have felt about the recklessness of administration policy, they were not prepared to sacrifice their access to military bases in Qatar, Saudi Arabia or Turkey to pressure their Middle Eastern allies.