CAIRO (Reuters) - Egyptians were electing a president freely for the first time on Sunday, making a daunting choice between a former general of the old guard and an Islamist who says he is running for God.
Many were perplexed and fearful of the future and signs were that, as in last month's first round, millions would not vote.
The contest, pitting Hosni Mubarak's last prime minister Ahmed Shafik against Mohamed Morsy of the Muslim Brotherhood, the veteran Islamist movement, is supposed to seal a democratic transition that began with Mubarak's overthrow 16 months ago.
But concern over a backlash among the disappointed losers saw the Interior Ministry put forces on alert across the country for the end of two days of voting at 10 p.m. (2000 GMT).
"We have to vote because these elections are historic," said Amr Omar, voting in Cairo, who called himself an activist of the youth revolution. Reluctantly putting aside misgivings about the Brotherhood's religious agenda, he said: "I will vote for Morsy.
"Even if it means electing the hypocritical Islamists, we must break the vicious cycle of Mubarak's police state."
But many other Egyptians, weary of political turmoil and the economic crisis it has brought, believe Shafik has the backing of the "deep state" - entrenched interests from the military to big business - and so may be better placed to bring prosperity.
Privately, officials from both camps suggested Shafik had edged ahead with five hours of busy evening voting still ahead.
The election comes amid a constitutional crisis and a stand-off between the ruling generals and the Brotherhood, which emerged from decades of repression under Mubarak and previous military leaders to sweep the parliamentary vote.
Those gains crumbled last week when senior judges, appointed under Mubarak, ruled that election void and the ruling military council dissolved parliament - a move met with only a muted reaction from many, who felt the Brotherhood had pushed its own particular interests too hard over the past few months.
Even the powers of the new president are unclear, though the military council was reported to be ready to award him some by decree this week - once it knows who the head of state will be.
OUTCOME UNCERTAIN
Egyptians massed in their millions against Mubarak in January last year in the hope that his removal would end poverty, corruption and police brutality. Many now seem tired of the social turmoil and political bickering that ensued.
"Egypt writes the closing chapter of the Arab Spring," read a headline on Sunday in independent newspaper al-Watan, which said the election offers a "choice between a military man who aborted the revolution and a Muslim Brother who wasted it".
The majority who voted for neither Shafik nor Morsy in a first round presidential vote last month now face what they see as a stale contest between a military establishment and its perennial foe which smothers hopes for a change for the better.
Many Egyptians may be staying away. But a sample of voter comments to Reuters near polling stations suggest many had put aside doubts about Shafik, whose campaign has gained momentum since he entered the race a few months ago as an outsider.
Waleed Mohamed, 35, voting in Cairo, said he chose Shafik, while his wife Hind Adel, wearing the full face-veil worn by some pious Muslims, has opted for Morsy.
"That's democracy for you," she said. "Everyone has their opinion ... No one knows who will win. God knows."
Monitors said they had seen only minor and scattered breaches of election rules by Sunday morning but not the kind of systematic fraud that tainted elections under Mubarak, despite mutual accusations of irregularities by the rival camps.
Monitors and vote officials said turnout seemed lower on Saturday and Sunday than in the first round ballot but said many people would arrive later on Sunday when the summer heat has abated. Voting concludes at 10 p.m. (2000 GMT), following a last-minute extension to deal with expectations of late voting.
A win for Shafik, 70, who says he has learned the lessons of the revolt and now offers security, prosperity and religious tolerance, may prompt street protests by the Islamists and some of the disillusioned urban youths who made Cairo's Tahrir Square their battleground last year.
UNEVEN OUTCOMES
Morsy has the backing of a movement forged by decades of clandestine struggle and from Egyptians who have put aside qualms about Islamic rule to block a return of the old regime.
Many see Shafik as the front man of a murky establishment determined to re-assert the power it wielded for six decades.
"Army rule is represented by Bashar al-Assad in Syria and represented in Egypt by Ahmed Shafik," said Amr Reda, an international law professor voting in Cairo for Morsy.
"We have had enough of military rule."
Morsy has failed to rally much public support from candidates who lost in the first round. To critics of the Brotherhood, it confirmed that the Islamist movement was too zealous and inflexible to represent all Egyptians.
"I will vote Shafik because I don't want anybody to impose on me a model of life that I don't accept," said health ministry employee Marianne Mallak, 29, voting in Alexandria. "I don't want somebody to rule the country in the name of religion."
Egypt's 10-percent Christian minority has come out strongly for Shafik, fearing religious oppression in an Islamist state.
Should Morsy prevail, he may be frustrated by an uncooperative military elite, for all the generals' pledges to cede power by July 1.
The military rulers ordered the dissolution of parliament, in line with last week's court ruling, an official said on Saturday. The decision enraged the Muslim Brotherhood, which said parliament could only be dissolved by popular referendum.
Dissolving the assembly "represents a coup against the whole democratic process", the group said on the Facebook page of its Freedom and Justice Party (FJP).
On Sunday, state-run Al-Ahram newspaper's website said the military would also issue a constitutional declaration within 48 hours to outline the president's powers, including appointing officials, calling parliamentary elections and outlining new rules for appointing an assembly to draft a new constitution.
Senior Brotherhood official Mahmoud Ghozlan, speaking to Al Ahram's website, said the ruling military council did not have the right to issue a constitutional declaration or make rules on how the constituent assembly should be formed.
SHOWDOWN
The Brotherhood hung back in the early days of the 2011 uprising and has sought to cooperate with the military's gradual shift to civilian rule.
But its gathering showdown with the military leaves Egyptians, Western allies and investors perplexed by the prospect of yet more of the uncertainty that has ravaged the economy and seen sporadic flare-ups in violence.
A gunfight killed two in Cairo overnight and 15 were injured, after a dispute between street vendors, a security source said. There was no apparent connection to the vote.
Police arrested 22 foreigners who were planning attacks after the election, another security source said. The Syrians, Jordanians and Palestinians were detained in Cairo on Saturday carrying "sophisticated weapons", the source added.
Shafik's supporters insist he and the ruling military council, which took sovereign powers when Mubarak quit, would work in harmony to restore confidence, notably for the vital and ravaged tourist trade. Morsy, they say, would struggle.
Egypt's armed forces have built up massive wealth and commercial interests, helped since the 1970s by a close U.S. alliance which followed the decision of the most populous Arab state to make peace with Israel.
Many Egyptians say the army, and its leader Field Marshal Hussein Tantawi, is just one wing of an entrenched security establishment that has resisted reform and oversight since Mubarak left and would wield influence long after the promised handover to an elected civilian by July 1.
"There is no doubt that the state in all its institutions - judicial, military, interior, foreign and financial - back Shafik for president and are working to that end," said Hassan Nafaa, a politics professor who campaigned against Mubarak.
"It is very difficult to eradicate this spirit of Mubarak."
(Reporting by Edmund Blair, Yasmine Saleh, Dina Zayed, Tom Perry, Tamim Elyan; Writing by Tom Pfeiffer; Editing by Samia Nakhoul and Alastair Macdonald)
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