Egypt's new president must limit his military's influence

Whatever happens in Egypt's presidential election, the real campaign, against entrenched military power in the state, will still have to be fought.

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Listening this week to an Arabic radio call-in show about the Egyptian presidential election, ahead of voting in the first round tomorrow, I noticed how much agreement there was. Most of the Egyptian callers wanted the president to focus on restoring security, rebuilding the economy and curbing the excesses of the Mubarak era, especially corruption and arbitrary decisions and detentions by the security apparatus. There was almost no talk of foreign policy, nor of questions of devotion, such as wearing the veil or adhering to principles of Sharia.

Analysts predict a likely showdown between two or three candidates for the presidency: a centrist liberal (former foreign minister Amr Moussa), a liberal Islamist (former Muslim Brotherhood member Abdel Moneim Aboul Fotouh), and perhaps a conservative Islamist (Mohammed Morsi, the Brotherhood's candidate).

Indeed, the shades of Islamism of the leading candidates have been heavily scrutinised: Mr Aboul Fotouh's line during a televised debate about his presidency giving "precedence" to Islamic "values and principles" was particularly dissected by the Egyptian blogosphere.

Once elected, the president will have to push the Islamist-dominated parliament to write a new constitution defining his powers and defining the role of Islam in politics. It is easy to characterise the coming political battle as one between Islamists and secularists.

Yet as the call-in show suggests, there is little appetite among Egyptians for prolonged political strife about the role of religion. Indeed, the real showdown in Egyptian politics is not between Islamists and liberals; it will be between the civilian government and the military. Dismantling the "deep state" of the military will be the bigger challenge, and touches on the issues that matter to Egyptians.

The Supreme Council of the Armed Forces (Scaf) has run Egypt since the toppling of Hosni Mubarak last year. So far, Scaf has presented itself as the guardian of "stability" in the post-Mubarak era, leading the country towards democracy. Once the new president is in place, Scaf is supposed to fade from the political scene. But don't expect the generals to go quietly.

For one thing, the new president will need to negotiate with them. Scaf will not simply step aside: it intends to "guide" the transition. Bear in mind that, back in November, Scaf tried to push through measures that would pre-determine how the writing of the constitution was run. Scaf wanted a guarantee that its military budget would continue to be secret and without government oversight, and that it could impose its own group to write the constitution if the first draft failed to pass the parliament. At that time, it was forced to back down because of renewed protests. But it will certainly try again.

Beyond Scaf, the military retains significant economic privileges. Every long-serving leader of Egypt since the end of the monarchy in 1952 has come from the military and each, in turn, has tried to cement the privileges of that group. That has led to the army exerting control over vast swathes of the economy - up to half, by some estimates.

In particular, the military runs factories, staffed with help from army recruits, that produce goods such as televisions and cars. Army generals own land and companies, and run all of these commercial interests away from the prying eyes of the government. The military will fight to maintain these privileges, and the very fact of these privileges, that economic weight, gives the military considerable resources with which to oppose the government.

The influence of the generals also extends into the shadowy mukhabarat, the interlocking security agencies that draw many of their recruits from the military and their authority, for now, from Scaf. How well the agencies will take a transition to civilian rule, and what influence the military men may still wield, will be difficult to assess. Under Mr Mubarak, and now, the security agencies continue to involve themselves in all aspects of civilian rule - everything from urban planning to cultural products has a security aspect. The military also retains a role in law enforcement, with trials of civilians in military courts continuing.

How to confront the military will be the biggest challenge for the new president. The Muslim Brotherhood, now the largest party in parliament and likely to garner significant support for Mr Morsi, has pursued an attempt to normalise relations with the military. Activists, particularly the unaffiliated who made up the bulk of Tahrir Square, accuse them of outright collusion.

These accusations, and indeed the temptation to side with the generals, will increase with an Islamist president and an Islamist parliament. A more liberal president, on the other hand, might lack the support base to be able to challenge the generals effectively, or may spend too much time arguing with an Islamist parliament.

The military has been an integral part of the leadership of Egypt since the monarchy was overthrown. If the polls are correct, the country's first democratically elected president will not be a military man. Dismantling Egypt's "deep state" will mean changes to security, to the economy and to the fight against corruption. The new president will need to do all of this while relying on the military for security. In order to rebuild a nation, Egypt's new president will need to dismantle a big part of the state.

On Twitter: @FaisalAlYafai