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Everything about Egypt's revolution has been unexpected, and the first-round results in the country's first-ever competitive presidential election are no different. The rise of former president Hosni Mubarak's last prime minister, General Ahmad Shafiq, who will enter the presidential runoff alongside the Muslim Brotherhood candidate Mohamed Morsi, has raised eyebrows across the political spectrum. So did the meteoric rise of the Nasserist candidate Hamdin Sabbahi to third place, and the fourth-place finish of Abdel Moneim Aboul Fotouh, who was backed by liberals and hard-line Salafi Islamists alike.

Egypt's voters overwhelmingly chose the revolution over the old regime and shattered the myth that the push for change is an urban, middle-class, Cairo-based phenomenon: The eight revolutionary candidates received more than 16.4 million votes. But their failure to unite on a single platform directly benefited Gen. Shafiq, who unexpectedly won 5.9 million votes (assuming no election-rigging).

Gen. Shafiq's success shocked many revolutionaries. "He is a murderer. His place is in jail, not on top of Egypt after the revolution," said one activist. Indeed, Gen. Shafiq has been linked to multiple cases of corruption and repression, including the "battle of the camels" on Feb. 2, 2011, when Mr. Mubarak's henchmen attacked Tahrir Square, killing and wounding protesters.

The rise of Gen. Shafiq is explainable in some areas. In Upper Egypt, "more than 60% of Copts voted for him," a source close to the Coptic Orthodox Church said, and in Coptic-majority areas the pro-Shafiq vote exceeded 95% because he is widely perceived as a bulwark against Islamism.

Moreover, many state employees (around 5.1 million of them are eligible to vote) and their families supported Gen. Shafiq, owing either to direct instructions from their bosses or to the perceived threat of creeping Muslim Brotherhood influence on government bureaucracies. And Gen. Shafiq received financing and support from Mr. Mubarak's National Democratic Party (NDP), as well as from business and security interests that benefit from the status quo.

But this was not enough to explain Mr. Morsi's defeat in the Muslim Brotherhood's traditional strongholds. In Sharqiya, a bastion of hard-core Muslim Brotherhood support with 3.5 million voters, Gen. Shafiq defeated Mr. Morsi by more than 90,000 votes. In Gharbiya governorate, another Muslim Brotherhood stronghold, he beat Mr. Morsi by more than 200,000 votes.

I compared the results with the Muslim Brotherhood's performance in the parliamentary elections earlier this year and found that the Brothers lost between 25% and 48% of their support in the Nile Delta (depending on the area), where 40% of Egyptians live. Assuming no foul play, Gen. Shafiq received around two million votes from four Delta governorates: Sharqiya, Gharbiya, Munufiya and Daqahliyya.

Egypt's Islamists – the strongest political force on the ground and the most repressed under Mr. Mubarak – have serious stakes in this election. But rather than uniting to improve their chances, their popular support was split among three candidates, two of whom – Mr. Morsi and Dr. Aboul Fotouh – placed among the four front-runners.

Salafi support for Dr. Aboul Fotouh, a moderate former Muslim Brotherhood leader, proved to be a double-edged sword, because it repelled many liberals and socialists who would have voted for him otherwise. Most revolutionaries who did not want an Islamist-dominated Egypt were alienated as well. Their votes went to Hamadi Sabbahi, from the left-leaning Nasserist camp, who surprised observers by winning 5.4 million votes.

If anything, the first-round results revealed the power of the non-Islamist revolutionary bloc, as well as Egyptians' willingness to punish Islamists for their weak job performance in the parliament. Indeed, six out of 10 Egyptians voted for Islamists in the parliamentary elections. That dropped to four in 10 in the presidential election.

Mr. Morsi, who finished first with six million votes, had the Muslim Brotherhood's disciplined, dedicated and experienced machine fully behind him. That meant a sophisticated election campaign that penetrated deeply into Egyptian society, urban and rural, and in which women played a key role. "This is where they beat the Salafis. Their women are experienced, outgoing, gutsy and trained to be convincing and charismatic," a Salafi activist who supported Dr. Aboul Fotouh told me. "Salafi women are shy, introverts. They can't compete for votes with the Muslim Brotherhood ladies."

The Muslim Brotherhood must now try to persuade the 10.7 million voters who supported Dr. Aboul Fotouh and Mr. Sabbahi to back Mr. Morsi in the runoff against Gen. Shafiq. The Muslim Brotherhood probably needs to reserve the vice-presidency for a non-Islamist like Mr. Sabbahi. Likewise, Dr. Aboul Fotouh, or perhaps the Nobel laureate Mohamed ElBaradei, will need to be appointed prime minister. Moreover, the Muslim Brotherhood will likely have to offer some concessions to guarantee balanced representation of Islamists and non-Islamists in the assembly that the parliament is to choose to draft a new constitution.

Whoever wins Egypt's presidency will face severe obstacles in challenging the status quo, owing to the dominance of the Supreme Council of the Armed Forces. The president's mandate was outlined by a constitutional declaration in March, 2011, but the SCAF has said that a more detailed one would be forthcoming after the election. That could mean weakening the president's powers and reserving some domains for the army – at least until a new constitution is adopted.

What remains certain is that no democratic transition can be complete without elected representatives exercising meaningful control over the security services and the armed forces. That will be the Egyptian revolution's ultimate test – and the most critical challenge for any president who does not embody a return to the past.

Omar Ashour is director of the Middle East graduate studies program, Institute of Arab and Islamic Studies, University of Exeter, and the author of The De-Radicalization of Jihadists: Transforming Armed Islamist Movements.

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