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A national flag waves as Egyptians line up outside a polling station to cast their votes during the first day of the presidential elections in Alexandria, Egypt, Wednesday, May 23, 2012.Khalil Hamra

Parishioners at the Church of St. Mark and Pope Peter in Egypt's second-largest city are giving thanks that Ahmed Shafik, a former Mubarak-era prime minister and the leading choice of Christians, did so well this week in the opening round of the country's historic presidential election.

They are also asking for divine assistance to make him victorious in the final showdown against Mohamed Morsi, an Islamic conservative.

"We want anyone but the Islamists to win," Georges Adel says as he shows a visitor around the massive white marble Coptic Orthodox church.

In the centre, he points out a shrine to the 23 parishioners killed last year when a car bomb exploded in the entranceway. There are large blood-stained shards from the church's façade, along with a shredded red dress and pictures of victims on the wall beneath a fresco of the open arms of Jesus.

The blast took place just three weeks before the popular uprising that triggered the fall of long-time president Hosni Mubarak, and was believed to have been the work of extremist Salafists – a puritanical sect that follows the ways of the earliest Muslims and disdains other religions.

Fear of such violence is why Christians across the country, as well as most secular Muslims, are relieved that it is no longer a forgone conclusion that Egypt's first freely elected president will be an Islamist. When 70 per cent of voters in the recent parliamentary election sent Muslim Brotherhood and Salafist Nour Party candidates to the People's Assembly, there seemed little reason doubt there would be such an outcome.

However, someone's prayers were answered – and now, instead, the country is starkly divided over which world view will triumph when the runoff vote on June 16 and 17 decides the ultimate victor.

The results have global implications because Egypt is not just any Arab state; it sets the political and cultural standard for all the others. Saudi Arabia has the oil, but the land of the Nile has the population – approaching 83 million – and the history. Much as its peace treaty with Israel, once scorned, has paved the way for others, the Arab Spring didn't bloom until the popular uprising reached Tahrir Square.

Now, as Arab countries from Tunisia to Syria turn out old authoritarian regimes and embrace an Islamist trend, Egypt stands in the middle with a foot in each camp. Will it complete the Islamist arc – or be the first to buck the trend?

Voters are being asked to choose between two very different options: On one hand, there is Mr. Morsi, a dour official of the Muslim Brotherhood. On the other, Mr. Shafik is a retired general, former head of the air force and Mr. Mubarak's pick to be prime minister at the time of last year's popular uprising.

Mr. Morsi espouses a speedy adoption of Islamic sharia law and a review of Egypt's 30-year treaty with neighbouring Israel, while Mr. Shafik – unapologetic about his role in the old regime – vows both to uphold the treaty and to halt the Islamists in their tracks.

It is hardly the choice for president the country's revolutionaries had in mind when Mr. Mubarak was ousted from power 15 months ago.

It is also a shock for the Islamists who saw the vote for all of them amount to less than 50 per cent, a major drop from the 70 per cent garnered by the Brotherhood's Freedom and Justice party and the Nour party in the parliamentary elections.

Many who voted for the Brotherhood before said this week that they did not want the group to control the presidency as well. Impatient for economic progress, some criticized the amount of time spent by the assembly on issues such as the role of women, divorce and genital mutilation, and blamed the Brotherhood for setting such an agenda.

'Is there anything better than Islam?'

Despite slipping, the Brotherhood still came out on top of the heap this week – there were 13 candidates in all – which stands as a testament to its depth and power. People were voting for the 84-year-old movement much more than for Mr. Morsi, its backup when the initial candidate was disqualified.

"He's part of an institution," Salama Mohamed Shehata explains. "I like the fact that he has such a big group standing behind him."

"The Muslim Brotherhood was not born yesterday," the 42-year-old Cairo court administrator adds. "They supported people long before this election."

The success also shows the deeply rooted identification with religion that many Egyptians feel. "Is there anything better than Islam?" asks a woman in Mataraya, a poor district with dirt roads on the northeastern edge of Cairo, enraptured after casting her ballot for Mr. Morsi.

Yet three-quarters of the electorate, including many Islamists, did not fall in line.

"Morsi is not the kind of leader Egypt needs right now," says Yasir al-Adel, a Nour party leader in Alexandria. "He's an executive, good at following orders. We need someone who is more open to other forces."

Mr. al-Adel says he had hoped that his Salafist movement would carve out a relationship with the new president, which is why the Shura Council of the Nour party voted 121-26 to back Abdel Moneim Aboul Fotouh, a former leader in the Muslim Brotherhood who left last year in a dispute over its dictatorial internal practices.

Unmistakable as a Salafist in the sect's trademark beard (longish with no mustache), Mr. al-Adel led a Nour team that worked the phones at the campaign's headquarters on Wednesday and Thursday in an effort to get out the vote. Dr. Aboul Fotouh's candidacy was characterized by its wide range of backers – from the Salafists to young revolutionaries, such as Google executive Wael Ghonim, who respect the candidate for his early commitment to the revolution and the six years he spent in prison for his views.

But not only was the Salafist support too late (the decision was made just three weeks ago), it may have been counterproductive. Young liberals reported being a little uneasy with someone also embraced by Salafists and the even more radical Gamaa Islamiya, which only recently renounced the terrorism that has made it infamous.

The late surge in support for another candidate, Hamdein Sabbahy, leader of the Nasserist party, may well have been the result of many Aboul Fotouh supporters seeking someone who was neither an Islamist nor a member of the old regime.

Just two weeks ago, when they met in the election race's only debate, Dr. Aboul Fotouh and former foreign minister Amr Moussa were considered the front-runners. Yet, when the ballots were counted, they finished fourth and fifth respectively.

"The debate was a debacle for both men," says Saeed Sadek, a political sociologist at the American University in Cairo. Mr. Moussa struck a fatal blow by exposing the long Islamist history of Dr. Aboul Fotouh, who in turn succeeded in depicting his rival as a relic of the Mubarak era.

"Morsi [the Brotherhood candidate]did the right thing by refusing to join the debate," Prof. Sadek says.

That Ahmed Shafik, an unrepentant military man, could come such a strong second speaks volumes of the fear that drove much of the electorate.

"We think he's the only one strong enough to enforce the law and stop the discrimination against us," says Fifi Roshdy, 48, a Christian in Imbaba, a religiously mixed Cairo neighbourhood, echoing the sentiments of Christians across the country.

Mr. Shafik also appeals to some Muslims because of his business experience as civil aviation minister, overseeing the transformation of Egypt Air to a world-class airline and building a fine international airport in Cairo. Meanwhile, others believe that he can restore law and order to a society that has witnessed a rise in crime and street riots.

But for many ordinary Egyptians, he is simply the antidote to their fear of the unknown. After decades of authoritarian rule, people want to stay with the devil they know.

The race boils down to a choice between two extremes

Ironically, at a time when Egyptians are just beginning the venture of democracy and would benefit from an inclusive administration, one in which most people would feel comfortable, they now must choose between two extremes.

One candidate stands for a heavy-handed religion-based approach to governance and is the chairman of the Muslim Brotherhood's Freedom and Justice Party, which already dominates the parliament. The other is a military-backed hardliner who would try to check the powers of the Islamist government.

Can the majority of Egyptians, who voted for neither, bring themselves to back either of them? Many young liberals will be tempted to boycott the runoff, in essence handing the reins to the Brotherhood, which would benefit by a reduced turnout.

But a victory by either side risks the loss of the liberal democratic values that Egyptians yearn for.

In the 15 months since Mr. Mubarak's ouster, most of Egypt's parties and political leaders have expressed support for the democratic project, says Bruce Rutherford, a Colgate University professor of Muslim politics and author of the 2009 book Egypt After Mubarak. This project foresees "an elected parliament that is fully empowered to draft laws, an independent judiciary that rules objectively and only according to the law, separation of powers, and firm checks on executive authority," he says.

At the same time, he says, "the strength of commitment to civil and political rights is not nearly so widespread."

For example, the Muslim Brotherhood seeks to repeal laws from the Mubarak era that broadened women's rights (particularly their right to divorce) on the grounds that these laws were imposed under foreign pressure. As well, it "ran very few women on its party's parliamentary list, and placed only five women on the short-lived committee of 100 persons tasked with drafting the Constitution," Prof. Rutherford notes.

The Brotherhood is keen to use the power of government to shape the morality of its citizens in matters of modesty, alcohol consumption and freedom of expression. It remains to be seen if it would be any more accommodating to Egyptian Christians than Salafists, who argue that non-believers must never have power over Muslims.

The former regime, which produced Mr. Shafik, may have a better record when it comes to women and religious minorities, but it was notorious for its heavy-handed and sometimes deadly suppression of free expression and assembly. Moreover, its commitment to democracy was limited, demonstrated by its refusal ever to permit truly free, fair and open elections.

There is one thing to bear in mind in the election of Egypt's president, Prof. Sadek says. "They are not choosing a pharaoh – the next president will have substantially reduced powers."

Indeed, the presidential powers have yet to be established, as they are to be determined by a constitutional assembly that also has yet to be agreed on. The Muslim Brotherhood controls parliament, so has a lead role in determining the assembly's makeup, but the Supreme Council of the Armed Forces will insist on a major say before turning over its executive powers.

Sadly, for many Egyptians, the joy they felt this week in casting the first ever truly free votes for a leader seems likely to be dashed, as a crisis is almost certain to erupt no matter who wins.

If the Brotherhood's Mr. Morsi wins, the military will resist giving up power and will make sure that the president is as weak as possible. Such a situation likely will lead to a confrontation.

If the veteran Mr. Shafik is victorious, military leaders may be pleased, along with fearful Christians like those at Alexandria's Church of St. Mark and Pope Peter. But the outcome could be serious civil unrest – people will take to the streets once again.

Patrick Martin is The Globe and Mail's Middle East correspondent.

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