Asmaa Waguih/Reuters
A man and a woman cast their votes in a school used as a voting center in Al-Arish city, north Sinai, Wednesday. Egypt's big battle is coming, as the third round of parliamentary elections wraps up today.

Egypt's big battle: Muslim Brotherhood vs. the military

Egypt's Muslim Brotherhood appears to have put up another strong showing in the last round of Egypt's parliamentary election – possibly enough for a parliamentary majority.

A big battle is coming in Egypt, as the third round of parliamentary elections wraps up today.

On one side is the Muslim Brotherhood, whose superior organization, brand recognition, and public trust made it the big winner in the first two rounds of voting. On the other side is the military junta that has ruled Egypt since Mubarak was forced from power, known as the Supreme Council of the Armed Forces (SCAF).

With the third round of the vote nearly done (though runoffs are still to come) the question is: Will the Muslim Brotherhood's Freedom and Justice Party (FJP) take an outright majority of parliament? And will SCAF continue to seek to limit the power of the parliament to write a new constitution?

The FJP, founded after Hosni Mubarak was ousted from power last year by Egypt's popular uprising, won 40 percent of the vote in the first two rounds and by some counts 48 percent of the available seats. They are expected to do well in today's final round, given as it's being held in smaller towns and rural areas. Depending on how this round shakes out after runoffs, and how potential legal challenges are dealt with, the Brotherhood could go over the 50 percent threshold.

If it doesn't make it, it will have to work with either the Salafis (Islamists who favor an austere application of Islamic law that they believe prevailed at the time of the prophet Muhammad) or secular parties to form a government. But either way, what will it matter? 

The Brotherhood has said it should be up to the democratically elected parliament to decide on the membership of a committee to write the new constitution, while the military has been pushing for appointees to be involved that would likely water down the Brothers' influence.

That Constitution will set the rules of the game for the new Egypt (for at least as long as it stands), and could have profound effects on the evolution of the state by what it says about the role of Islam, protections of minority rights versus the will of the majority, and how much civilian control can be exercised over the military.

Generals have been the most powerful de facto politicians in the country since the '50s, with both Mubarak and his two predecessors drawn from the officer corps. The military has been eager to maintain control over its own budget – and over its vast array of business interests.

The military's ability to get its way, however, is unclear. Writing at the Middle East Research and Information Project Issandr El Amrani argues that the military, due to a variety of missteps since February, has squandered a lot of popular support. He writes:

The military’s claim to be guardian of the revolution has been weakening since soon after Mubarak was toppled. The SCAF was slow to arrest kingpins of the old regime, and its military police maltreated protesters in March and April, as with the infamous “virginity tests” of women. The protest movement’s mounting dissatisfaction culminated in the reoccupation of Tahrir Square in July. Another turning point was the October 9 confrontation at the state broadcasting headquarters, known as Maspero, in which 25 protesters for Coptic rights died at the hands of army troops. (The SCAF claims that an unknown number of soldiers were also killed; [blogger Alaa] Abdel Fattah is accused of murder in this connection.) If many Egyptians accepted that these deaths resulted from panic among the soldiers, the SCAF’s grip on public sympathy has slipped badly amid the clashes of November and December.

But that does not necessarily mean that the Brotherhood will have it all its own way. During the popular street protests this fall, the Brotherhood stood apart, afraid that unrest could lead to a cancellation of elections and a loss of its chance to seize power. In that, it looked like it was backing the military. The movement will be somewhat constrained by the reality of the military's power within the country – and the chance that its opponents, particularly some of the secular parties, will look to the military to protect their own interests.

In the months ahead, we'll find out if the Brotherhood is willing to cut deals with the current powers that be (it has in the past). But either way, this election, with all its flaws, has shown a movement that was still officially outlawed when Mubarak fell is today the most popular political force in the country.

Follow Dan Murphy on Twitter.

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