Muslim Brotherhood candidate Mohammad Morsi’s victory in the presidential election widens Egypt’s democratic opening by a crucial, if narrow, margin. But a long and difficult struggle lies ahead before democratically elected civilian leaders can assert meaningful authority over the country’s armed forces. Without this, future governments will lack the genuine autonomy to devise and implement policies, and will remain chronically unstable.

Yet former regime supporters, illiberal secular politicians, and even some liberal figures are confident that Morsi will last no more than a year, let alone a full four-year term. They further expect the ruling Supreme Council of the Armed Forces (SCAF) to manipulate the drafting of the new constitution and the election of a new parliament in the coming months so as to ensure that Morsi will be no more than an interim president. Should the SCAF succeed, Egypt will come under indefinite military custodianship.

The publication of the amended constitutional declaration by the SCAF on June 17, 2012, is telling of what lies ahead. For all intents and purposes, the SCAF pressed the “reset” button, cancelling all of the transitional arrangements, timetables and outcomes of the preceding sixteen months — except for the presidential elections. The SCAF also effectively decreed a second interim phase that will last for at least the first six months of Morsi’s presidency. Moreover, the SCAF acted unilaterally, without any attempt to consult the political parties or presidential candidates as it had done in the past. This underlines its special position as the most powerful political actor in Egypt, but also suggests that it believes it is approaching the endgame, and that it must start laying its cards on the table regarding the constitutional prerogatives and exceptional status it seeks to perpetuate.

The manner in which the SCAF has devised the second interim phase will award it two significant points of leverage over the coming process. First, the constitution must be ratified before the parliament — ordered dissolved by the Supreme Constitutional Court on June 14 — can be re-elected. Parliamentary leaders have applied to the State Administrative Court to reverse this decision, but if it stands, Morsi will be denied the support of an important political ally and major institutional player in shaping the new constitution. And without a parliament in session, it is unclear who now has the authority to confirm the next government: Morsi has the power to appoint the prime minister, but the SCAF will probably once more claim the right to confirm the council of ministers, further extending its power.