Mohamed Morsi victory is a landmark for Egypt – but a qualified one

Muslim Brotherhood candidate's win is the best outcome of an election that leaves the military as the power behind the throne

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Egyptians celebrate Mohamed Morsi's victory in Tahrir square
Egyptians celebrate Mohamed Morsi's victory in Tahrir square. Photograph: Khalil Hamra/AP

In the end, of course, only one candidate could win – though the cliffhanging, nail-biting tension was maintained until the very last moment. Victory for Mohamed Morsi in Egypt's presidential race is a landmark in a dramatic post-revolutionary transition and a defining event of the Arab spring.

For the man representing the Muslim Brotherhood, the world's oldest Islamist movement, to win a free and fair election for the presidency of the Arab world's most populous country is a triumph that will resonate around a turbulent region. It will be recognised as an historic achievement. But it is a flawed and qualified one.

Morsi will be Egypt's first civilian president since Gamal Abdel-Nasser and his fellow officers overthrew the monarchy in 1952. Hosni Mubarak was forced to quit in February 2011 though the generals who had backed him stayed on. Morsi's biggest problem is that the military are still there – the real power behind the throne.

Still, much about Egypt is already different. Expectations of change are now greater than before the great drama of Tahrir square began last year. It is not possible to go back to "square one." But political polarisation is clearer too: no one should underestimate the impact of the Brotherhood's success for a movement that was suppressed and feared for decades. The defeated Ahmed Shafiq, Mubarak's last prime minister and the candidate seen as representing the old regime, still won 48% of the vote. It was, for many millions of Egyptians, a choice between unpalatable extremes.

Morsi's victory followed parliamentary and presidential elections that were freer and fairer than anything in the preceding 60 years, though for some the whole process has always been a sham: "Wow, all this suspense in this joke of an election, imagine if it was actually real," tweeted one cynic before the result was announced on Sunday.

But the vote-rigging of the Mubarak years has given way to fixing at a higher level. Egyptians describe a "soft coup" anchored in a constitutional declaration that gives the supreme council of the armed forces (Scaf) unprecedented powers after a court ruling dissolved the Islamist-dominated parliament. The new constitution, crucially, remains to be written. Morsi's own authority looks like being extremely limited.

The secrets of behind-the-scenes bargaining between the Brotherhood and Scaf remain to be told. It will be surprising if the generals do not retain their financial clout and privileges, and their powers to make war, conduct foreign policy and maintain internal security – the holy trinity of Egypt's deep state. It will suit them perfectly to blame the civilian president for the parlous state of the economy.

In a curious twist of recent days, Shafiq supporters accused the US of quietly encouraging a Morsi win – as a way of cementing the dominance of Scaf and securing the strategically important peace treaty with Israel.

On balance, Morsi's victory is the better outcome. It creates the possibility of continued bargaining between the army and the Brotherhood, whose well-organised rank and file remain ready to take to the streets to maintain pressure on the generals. A Shafiq win would have immediately reignited protests and made it easier for the army to crack down in the name of stability.

Morsi's biggest challenges start now. Will he stand up to the army? His claim to represent "all Egyptians" will be tested by how he reaches out to the liberal and independent candidates who fell away in the first presidential round.

Who will he choose as a prime minister? A non-Brotherhood figure – Mohamed ElBaradei is being mooted – could signal pluralism and help deflect heat on the economy. Nervous Copts and women will need reassuring. Not everyone believes the Brotherhood's newfound spirit of inclusiveness: after all, it backed Scaf's transition plan for most of last year and then reneged on its own promises not to field too many candidates for parliament or any for the presidency.

Morsi's victory is not the end of Egypt's turbulent post-revolutionary game. But it is perhaps the end of the beginning.

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