The SCAF and the Brotherhood also differed constantly over the timing of key steps in the transition process. For example, Islamic and liberal parties disagreed on whether to draft the new constitution before or after parliamentary elections. Liberal political parties pushed to draft the constitution prior to the elections to mitigate fears that sharia would become the basis of legislation in a Brotherhood-dominated parliament. Conversely, the Brotherhood expected to win the elections and thus wanted to be in a position to control the constitution-drafting process. The SCAF used this debate as an opportunity to push once again its supraconstitutional principles, which would go into effect immediately and set the benchmark for any future constitution. Instead of creating a meaningful compromise, this proposal angered the Brotherhood because it showed the SCAF’s intention to influence the constitution regardless of who eventually was selected to write it. According to recent reports, the SCAF did this in order to preserve its corporate interests and to ensure the secular identity of the Egyptian state in the context of a Brotherhood-dominated government. Indeed, one Egyptian jurist went so far as to say that the military and the Supreme Constitutional Court colluded in an effort to protect the constitutional process from being hijacked by the Islamists. Anwar el-Sadat, a nephew of the former president and a member of the disbanded parliament, summarized this sentiment when he said that the generals “want to make sure before they leave that the Constitution is not monopolized by any group or direction. They would like to make sure [Egypt] is a civil state.”

The most serious crisis of the postrevolution transition occurred in June 2012, when the Supreme Constitutional Court, appointed by Mubarak and generally perceived to be acting in concert with the military, dissolved the popularly elected parliament. Jurists noted that the SCAF structured parliamentary elections in such a way that would allow it, working alongside the judiciary, to negate the results at any time by applying previous legal precedents. Many speculated that this move was another attempt to reestablish a military-backed, autocratic government and a means for the military to fix the election in favor of Ahmed Shafik, a former air force commander who ran on a law-and-order platform. Shadi Hamid, research director of the Brookings Doha Center in Qatar, summed up fears over the court’s decision: “From a democratic perspective, this is the worst possible outcome imaginable. This is an all-out power grab by the military.”

The SCAF further fueled speculation about its intentions to consolidate power when it reinstated the principles set forth in the Selmi document just before the presidential election. This declaration reimposed martial law, removed military decisions from public or government accountability, and gave the military formal oversight of the political system. Critically for the presidential election, the president was removed as head of the SCAF and presidential powers were significantly limited. The SCAF also announced the creation of a national-security council that, while nominally under the chairmanship of the president, would have a majority of military-appointed members.

After a period of intense behind-the-scenes maneuvers and negotiations between the SCAF and the Brotherhood, the Supreme Elections Committee in late June announced Mohamed Morsi, the Brotherhood’s candidate, as the winner of the presidential election. Morsi promised to represent all Egyptians and to appoint a unity cabinet. The military promised to return to the barracks. Yet the future of military-Brotherhood ties and the military’s ambitions remain uncertain.

THE PROSPECT of serious change in Egypt—meaning the building of a democratic culture and democratic institutions—depends to an outsized degree on the future attitudes and actions of the Egyptian military. In most respects, it has been comfortable with the regime and the nature of the political system over the past sixty years, since the 1952 revolution. While there were moments of tension between the political and military elites during that time, none of these minicrises threatened to redefine the very nature of politics. Nasser and Abdel Hakim Amer dueled over who would be preeminent in decision making. Sadat and the leaders of the “centers of power” revolt in 1971 wrestled for political power. Mubarak dismissed Defense Minister Abdel Halim Abu Ghazala in 1989 not only on charges of corruption but also because Abu Ghazala appeared to be a competitor for power. Field Marshal Mohamed Hussein Tantawi and the military brass pushed Mubarak aside in 2011 largely in order to preserve the regime, not to uproot it. Thus, relations between the military and the political leadership have not always been smooth, but the two coexisted as partners in arms. The challenge ahead is whether the military can abide the kinds of systemic changes that a Muslim Brotherhood–led government and parliament would implement in the truly revolutionary, regime-changing phase of the Egyptian uprising that began in Tahrir Square.

At least four barometers will be instrumental in assessing the military’s acceptance of political change. Most important will be the nature of the system of politics and the controlling regime that emerges in the months ahead, both with regard to the military’s autonomous position in society and the preservation of a secular regime. As this article is being written, there is great uncertainty whether new elections for parliament will be necessary, under what conditions a new constitution will be drafted, and whether street violence and pressure will affect the transition to civilian rule. Each of these issues will pose tactical choices for the military and will influence the future direction of politics and the nature of the Egyptian state. In a large, strategic sense, the military will evaluate its course of action on these and related issues according to a simple metric: Will the proposed course of action fundamentally alter the system in a manner that erodes the military’s special place and role in society?

The military’s interest in the nature of the regime should not be confused with its insistence on actually governing. Steven Cook of the Council on Foreign Relations got it right some years ago when he argued that the military wants to rule but not govern. This remains the case today, notwithstanding the temporary detour that the SCAF took in actually governing. (Indeed, that experience likely reinforced the military’s distaste for politics.) Although the SCAF may not want to govern, it does want to maintain power—particularly with regard to drafting the constitution—in order to establish an institutional framework that preserves the secular nature of the state, irrespective of who is elected to the parliament and the presidency.

A comfortable regime for the military would look a great deal like the system of the past decades with, perhaps, a greater degree of democratic messiness. Parliament will be vocal; the new president will try to preside but under the watchful and skeptical eye of the military; the judiciary will flex the muscles it long has wanted to in order to ensure its independence; and civil society will remain restive. All of this probably would fall within the comfort zone of the military, especially if the focus of political activity is domestic—the economy, social issues and the like.

A related issue for the military will be the degree to which its corporate interests and self-defined position as the embodiment of the 1952 revolution remain unaffected. For a military that has not had to fight since 1973—not counting the expeditionary nature of Egypt’s role in the 1991 Gulf War—the Egyptian officer corps has maintained its esprit de corps largely on the basis of its foundational role in the modern history of the country. When the youthful Tahrir protestors recognized this at the outset of the 2011 uprising, it was a brilliant tactical nod to the most important player of all. Eighteen months later, the youth and the military know that such recognition is no longer so easily assured, but for the military, it is no less important.

In practical terms, the military will define this issue on the basis of how much independence it retains in the budget process and in defining national-security policy for the country. The military will not permit civilian control over its budget, and it will balk at almost any effort by civilians to exercise oversight. Since this is a benchmark for democratic evolution, there is sure to be a titanic clash over this issue in the period ahead.

Regarding national-security policy, the recently revived national-security council will be staffed largely by military appointees. While the new president is likely to be given some leeway in some aspects of foreign policy—just as Mubarak often allowed the foreign ministry to play a nearly independent role at times—the military will draw the line on issues that impinge directly on national security. In practical terms, this means an outsized role for the military on issues related to Israel, Libya, Sudan, Iran, intelligence cooperation and U.S. relations. The bottom line for the military will be its insistence on a veto over any decision to deploy troops or declare war.

In addition to relative autonomy over its economic empire and national security, a second barometer of military attitudes will be the actual policies undertaken by the new Egyptian government. The military establishment has made clear it will not countenance a return to a state of war with Israel. The Egyptian-Israeli treaty and relationship, for all their problems and unpopularity on the Egyptian street, have been the cornerstones of Egypt’s strategic outlook for the past three decades, and this is not likely to change in the foreseeable future. The military will not balk at a cooling off of relations or a tougher Egyptian diplomatic stance toward Israel, especially on the Palestinian and nuclear issues. But the military will draw a deep line in the sand when it comes to possible unilateral moves to change or abrogate the treaty.