This week, Egyptians will elect a president for the first time in their history. Since 1953, the year in which Egypt became a republic, the country’s presidents have been no more than military dictators in civilian attire. Sadly, the revolution that ousted president Hosni Mubarak last January did not mark the end of military rule.

Former foreign minister Amr Moussa and former prime minister Ahmed Shafiq are the last candidates standing—that is, the last candidates the ruling Supreme Council of the Armed Forces hasn’t managed to invalidate or force out. Though Moussa is more neutral toward the military and the security establishment, he wisely distanced himself from the old regime, while Shafiq served Mubarak as prime minister until the very last minute.

The winning candidate will need a political machine of national reach, and the best-qualified groups remain the remnants of the old regime and the Muslim Brotherhood. The military elites will demand widespread immunity from prosecution, and if either Moussa or Shafiq become president, they’re likely to get it. Otherwise, the army will be forced to cut an improbable deal with an Islamist president.

Egypt does not yet have a new constitution, and it remains anyone’s guess what powers the president will have. Egyptians don’t even know whether the new regime will concentrate executive powers in the president or the prime minister, so they have no idea if the man they’re electing will even be able to implement political reforms.

The army has proceeded with the assumption that any president, however powerful, constitutes a threat. Since February 2011, the generals have succeeded in frustrating every single political group. In banning most popular presidential candidates or deterring them from running, the army has left Egyptians of all ideologies with their second-best choices.

In mid-April, a ruling by the electoral commission—whose members were picked with the army’s approval—banned the ultraconservative Salafi candidate Salah Abu Ismail.The commission also banned Muslim Brotherhood financier and strong man Khairat el-Shater. And the secularists watched helplessly as the army boxed in former International Atomic Energy Agency head Mohamed ElBaradei and left him no choice but to withdraw.

The Brotherhood chose Dr. Mohamed Morsi, the leader of its Freedom and Justice Party, a less powerful and charismatic man than el-Shater. The Salafis settled for Dr. Abdel Moneim Aboul Fotouh, an Islamist who began his political life as an ultraconservative and has over the years moderated to the point that he appeals to many liberals. Yet, Aboul Fotouh is neither a hard-core Islamist nor a liberal, and while he has supporters in both groups, he appeals fully to none.

In the secularist camp, both Moussa and Shafiq purport to defend the modern state, security, and stability while carrying out a genuine democratic transition. For the democratic reformers who organized the revolution, these men are far from ideal choices, but they may yet counter the rise of the Islamists.

Whoever he is, Egypt’s new president will face a crisis of legitimacy and will have to work hard to convince people he will be fair to all political groups. Assuming he has real powers, he must focus his energy on crafting a constitution that includes Islamists and secularists while protecting women’s and minority rights and creating a truly democratic state.

The new president will have to win over Egypt’s most vital political constituencies one by one. First, he’ll need to manage the relationship with the military, giving it substantial space and autonomy while ensuring that Washington and other foreign powers conduct political business solely through the civilian government.

The United States and other allies can, of course, conduct military-to-military relations as usual, but they must respect a separation of powers inside Egypt. This will be difficult but not impossible.

In the late 1990s, the Turkish army looked to circumvent proper diplomatic channels to Clinton administration officials in hopes that they would acquiesce to a military coup, and they wisely had none of it.

With that, the new president will gain international legitimacy. From there, he will face the still-daunting challenges of strengthening state institutions like the legislature and the judiciary while ensuring that each has an incentive to respect the new constitution.

If the new president fails to put the military in its place—in a manner the generals can accept—Egypt will face continued instability. More likely than not, that will mean worse to come.

Khairi Abaza is a senior fellow at the Foundation for Defense of Democracies and a former official in Egypt’s Wafd party.

Image: Jonathan Rashad