This policy challenge comes just as the Obama administration’s entirely new international security team – secretary of state, secretary of defence, UN ambassador, CIA director and national security advisor – is about to settle in, replacing the older hands in place during the first administration.

John Kerry has replaced Hillary Rodham Clinton in Foggy Bottom; Chuck Hagel stepping in in place of Leon Panetta at the Pentagon; John Brennan in place of General David Patraeus at the CIA; Susan Rice to take over from Tom Donilon as national security advisor and Samantha Powers to replace Susan Rice at the UN as soon as her confirmation from the Senate occurs.

It is entirely possible this team will be somewhat more sympathetically attuned to be interventionist in cases where such efforts can be couched in humanitarian engagement terms. Powers, for example, was a strong advocate of US involvement during the Rwandan killings and in the Eastern Congo (although Susan Rice has strong ties to Paul Kagame’s Rwanda).

By the same token, this new team is rather less likely to be a proponent of broad new, sweeping engagements around the world. This is a politically astute group thoroughly conscious of the budgetary limits, the lack of a political consensus within Congress, and – above all – a severe lack of national public support for such adventures in Africa, the Mediterranean or South Asia unless there is an overwhelming, impossible to avoid case of there being a direct, immediate threat to the US itself. There is one exception, of course, and that is finding a way to counterbalance a surging China – but doing it without resorting to direct military confrontations.

However, Egypt’s current agonies present the Obama administration with a whole series of choices, virtually all of them bad, with extra-large implications for the success of the future of the Obama administration’s foreign policy architecture – and legacy. And the situation is not a simple one of supporting humanitarian intervention or stark human rights choices. And it is very difficult to place the immediate circumstances of this on either of Obama’s two predecessor administrations of George W Bush and Bill Clinton.

Following four wars between Israel and Egypt – 1948, 1956, 1967 and 1973 – in which the US was informally allied with but strongly supported Israel versus Soviet support for Egypt, The United States and Egypt began their cautious rapprochement during Anwar Sadat’s presidency in the late 1970s that eventually led to substantial economic support aid as well as military assistance, once Egypt and Israel had moved towards a peace accord. This aid from the US to Egypt stabilised the country’s economy and allowed for a regimen of steeply subsidised prices for basic commodities that also contributed to social stability.

On the other hand, the growing relationship between the US and the Egyptian military helped keep the military afloat and armed for decades – bolstering the military’s own proclivities for broad, wide-ranging power in the country’s polity, its increasing penetration into the economy and its very strong sense of itself as the definer and protector of Egyptian nationhood and sovereignty – and helped keep the nation’s political life frozen in time. This growing US connection to Egypt also contributed to substantially stabilising the Egyptian-Israeli border, a key US policy goal in the region, once that peace accord between the two Middle East powers had been signed.

The current problem for the Obama administration vis-a-vis Egypt began in the Arab Spring of two and a half years earlier. (Some would argue, of course, that this problem had also begun several decades earlier as a result of that increasingly close connection to the Egyptian military.) But, caught off guard like almost everyone else by the sudden ferocity of the Arab Spring, it appeared that the Obama White House temporised about whether, or how, it should put its weight and influence behind Hosni Mubarak’s then-tottering regime – or cut off its umbilical cord and then endorse or even embrace the citizen revolution unfolding in Tahrir Square, live on international television and on the Internet.

The logic of the Obama administration’s rhetoric that “the era of the big man in Africa is over” would seem to have directed it towards such a major policy reorientation. But this was checked by the argument that the whole, carefully constructed architecture of Middle East stability was predicated on the rule of the octogenarian Hosni Mubarak and the military’s own even longer run in power back to the 1950s. As a result, the Obama administration essentially equivocated at first, giving Egyptians of all orientations a sense that while Washington might be reluctant to stay the course with its long-time friend, the ruler of Egypt, it also was unable to throw itself fully behind the new forces at play that would seem to have spoken the language of greater democratisation, primarily because Washington was unable to calculate where such developments would ultimately lead for the rest of the region.

Then, as the Muslim Brotherhood began to assert a primacy in the civilian political sphere and gain the presidency in the country’s first real open election with its candidate, Mohammed Morsi, it seemed the country was settling into a new, still turbulent, but increasingly predictable phase. In the new nationalist climate in Egypt, Egyptians and Americans had butted heads over American staffing and funding of NGO groups.

Then there were disagreements about the nature and continuation of US military assistance and those were followed by a violent protest against the US Embassy in September, following the release on the Internet of a film trailer designed to defame Islam (and presumably made by a Coptic Egyptian based in the US). Regardless of all of this, American policy makers and Egyptians seemed to be making a bumpy transition towards a new reality. Egypt seemed to be evolving an uneasy balance between more secular modernists, the military and Muslim Brotherhood supporters; but from the American policy maker’s perspective, the essential continuity of Egyptian policies internationally seemed to be holding – wavering and wobbling a bit – but holding.

When the newest protests in Cairo by enormous gatherings of opponents to the Muslim Brotherhood-led government led to the overthrow of the Morsi administration by the military, the Obama administration was reluctant to label what had just occurred as a coup d’état, despite its obvious appearance of being just such a thing. Egypt’s military has now imposed an interim government under Adly Mansour, a chief judge of the country’s high court, reportedly arrested Morsi and other top officials of the Muslim Brotherhood, but it has also said new elections would take place some months off in the future. This latter has not yet mollified many of its critics in the US – or obviously among the Muslim Brotherhood’s supporters. As if to balance this, however, Mohamed El-Baradei, possibly Egypt’s best-known figure outside the country, has urged a positive stance towards the military’s move by other nations.

For American policy makers, one challenge is that if they publicly define what has happened as a coup, pure and simple, US law (a clause in the appropriations act that governs military assistance) would require a cessation of military assistance until civilian rule is re-established. But some argue that cutting military assistance would, presumably, only lessen American leverage with the very military receiving that assistance on the grounds that once cut loose there would be no way to rein them in.

Observers also note that the US’ apparent inability to press the military very much to restrain themselves in the public political sphere (or the US’ inability to bring much influence to bear on the Muslim Brotherhood or even the people opposed to them) is a further sign of America’s diminishing influence on the pace of events in Egypt – or any of the actors within it.

For its part, while the US continues to insist it is not taking sides in Egypt’s unrest, it is also true that just before General Abdul Fattah al-Sisi declared the takeover, State Department spokesperson Jen Psaki strongly criticised the Morsi government and spoke gently about the military, calling out Morsi for failing to address the demands of the protesters in his speech the night before the generals moved – even as Psaki failed to criticise the military’s coup threat. This seemed a real shift in America’s position as it was up until a few weeks ago when American diplomats did about as much as they could do to avoid criticising the Morsi government.

As Psaki told journalists, “It’s important for President Morsi to listen to the Egyptian people and take steps to engage with all sides. Unfortunately… He didn’t do that in his speech last night.” And when Psaki was asked if she would condemn General al-Sisi for pledging to overthrow Morsi’s elected regime “with our blood”, she refused to do that and replied, “We believe all sides need to take steps to talk with each other to engage with each other to lower the level of violence.” When an incredulous reporter asked if the US was not going to condemn the military’s ultimatum to the president, the spokesperson replied, “correct”.

If the American goal is to cosy up a bit to the incoming political realities in Egypt, this may have succeeded, but it does beg the question of the longer-term impact of such a stance. After these State Department statements, Foreign Policy magazine commented on Wednesday that “Which way Washington is leaning looms large as US officials try to avoid alienating the ruling Muslim Brotherhood without betraying the aspirations of Egypt’s liberal opposition, who could come out on top in the days and weeks to come. Already, the Obama administration has taken flack for repeatedly waiving restrictions passed by Congress on aid to Egypt and failing to loudly criticise Morsi’s repeated power grabs.”

This may now mean the US felt the coup – or whatever they chose to define it as – was an inevitability and that the US must try to build a relationship with the new political realities on the ground. In the fast-moving events, however, late news indicates Barack Obama’s administration now says aid to Egypt is now under review after all.

Concurrently, the Obama administration has been taking shots from Republicans such as Texas Senator Ted Cruz and House Foreign Affairs Chairman, Republican Congressman Ed Royce who have charged US Ambassador to Cairo, Ann Patterson, was the key implementer of policies that had been providing US support to that unpleasant Muslim Brotherhood. For example, Cruz wrote on Wednesday, “As opposition to Morsi coalesced around the Tamarod movement [the anti-Muslim Brotherhood movement], the Obama administration missed the opportunity to support its efforts and further the vital interests of the United States without firing a shot. Instead, the sole priority seems to be to defuse the situation and preserve the status quo. Ambassador Patterson has assumed the leading role in implementing this policy, meeting with members of the opposition not to encourage them to pursue a true secular democracy in Egypt but to try to persuade them to tone things down.”

Going forward, Egypt’s agonies may foreshadow further difficulties for Muslim Brotherhood-style parties in places such as Libya – and even the loose alliance of insurgents in Syria. The challenge for American policy makers is that this continuing, rolling instability in Egypt and on-going conflict between “modernist” forces and Islamists may unnerve the Israelis and have them put their military at a higher state of readiness, give comfort to the Syrian government of Bashar al-Bashar, unsettle America’s remaining allies in the Arab world (Saudi Arabia, Jordan and Bahrain) – or even stiffen the resolve of Iran to continue on its presumed course towards nuclear weapons development to counter the reverses of the Muslim Brotherhood in Egypt.

All of this simply underscores the essential importance of Egypt in the Middle East and the Arab and Muslim worlds. An unravelling in Egypt will have large repercussions throughout the broader region, making it even more complicated for a US that is so deeply involved in the region to figure out who to back, which developments to encourage or discourage – or, in fact, how America can use its increasingly limited influence for any goal. The Obama administration is going to be spending a great deal of its foreign affairs attention on trying to guess what will work for US-Egyptian and US-Middle East relations in years to come. DM

Read more:

• New Egypt president Adli Mansour promises early elections at the Financial Times;
• Morsi Aides Arrested in Widening Sweep in the New York Times;
• Egypt’s Arrests of Islamists Pose Test to U.S. Over Military Aid in the New York Times;
• ElBaradei Seeks to Justify Ouster of Egypt’s President in the New York Times;
• Morsi’s Fall in Egypt Lauded by Syria’s Assad in the New York Times;
• Muhammad Morsi was incompetent, but his ouster should be cause for regret, not celebration in the Economist.

Photo: Army soldiers stand guard near a supporter of ousted President Mohamed Mursi at Cairo University in Giza, on the outskirts of Cairo July 4, 2013. The leader of the Muslim Brotherhood was arrested by Egyptian security forces on Thursday in a crackdown against the Islamist movement after the army ousted the country’s first democratically elected president Mursi. At least 16 people have been killed and hundreds wounded in street clashes across Egypt since Mursi’s overthrow. The words on the poster read, “Yes to legitimacy”. REUTERS/ Asmaa Waguih.