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The rise of Shafiq is explainable in some areas, but raised eyebrows in others. 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 was widely perceived as a bulwark against Islamism.

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

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

I compared the results with the MB'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, 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 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 – Morsi and Aboul Fotouh – placed among the four front-runners.

Salafi support for Aboul Fotouh, a moderate former MB 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 ten Egyptians voted for Islamists in the parliamentary elections. That dropped to four in ten in the presidential election.

Morsi, who finished first, with six million votes, had the MB'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 Aboul Fotouh told me. "Salafi women are shy, introverts. They can't compete for votes with the MB ladies."

The MB must now try to persuade the 10.7 million voters who supported Aboul Fotoh and Sabbahi to back Morsi in the runoff against Shafiq. The MB probably needs to reserve the vice presidency for a non-Islamist like Sabbahi. Likewise, Aboul Fotoh, or perhaps the Nobel laureate Mohamed ElBaradei, will need to be appointed as Prime Minister. Moreover, the MB will most 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 (SCAF). 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.