Leading article: The storm clouds are gathering over Egypt

When mass protests toppled Hosni Mubarak in February last year, Cairo's Tahrir Square swiftly became the emblem of the hopes of the Arab Spring. Sixteen months on, however – with the constitution still not written and soldiers guarding the doors of the parliament – the outlook for the Egyptian revolution is far from certain.

There were always going to be hiccups. After six decades of military rule, three of them under Mr Mubarak, dismantling the old power structures – the so-called "deep state" – could hardly be expected to run entirely smoothly. But all the signs suggest that the ruling military council is tightening its grip on power just as the time to relinquish it is approaching.

It is true that the Supreme Council of the Armed Forces (SCAF) has restated its commitment to hand control to the new President at the end of this month as planned. But on Sunday night, a bare few hours after the polls closed, the council issued a constitutional declaration granting itself both sweeping legislative and budgetary oversight and also, crucially, the final say over who will draft the constitution that will set out the President's powers.

Coming just days after the Muslim Brotherhood-dominated parliament was declared unconstitutional and dissolved, it is hard to avoid the conclusion that the military is consolidating its position while it can. The decision that the army will remain outside presidential control, and that parliamentary elections will not go ahead until after the constitution is in place, only add to moderate Egyptians' fears. It is understandable, then, that the council's actions were swiftly branded a "coup", and that there was a smattering of demonstrators back in Tahrir Square yesterday.

In response, there was much bluster from the council, not least the claim that the situation is being "blown out of proportion". For such protestations to have any credence, however, will take action as well as words. Until then, it is, alas, Nobel laureate Mohamed ElBaradei's verdict of "a grave setback for democracy" that stands.

But it is not only the machinations of the military council that are disquieting. A presidential race that, by the final round, pitted Mohamed Morsi, of the Islamist Muslim Brotherhood, against Ahmed Shafik, a former air force commander and Mr Mubarak's final Prime Minister, has only added to the frustrations of the young, liberal demonstrators who led the Tahrir Square protests. To many, such a choice looks like the revolutionary momentum is all but lost.

The election has certainly proved a close-run thing. So much so that both sides are making early claims of victory, ahead of Thursday's official result. Although neither candidate merits unqualified support, it is Mr Morsi who must be preferred of the two. The election of Mr Shafik simply looks too much like a return to the bad old days, even more so in light of the military's latest moves.

That said, a Morsi presidency carries significant risks of its own. For all his efforts to cast himself as a liberal, the prospect of Islamist rule remains a disconcerting one. More concerning still, given recent developments, is that Mr Morsi may prove no more effective a break with the past than Mr Shafik. The Muslim Brotherhood was a latecomer to the protest movement, and has been a vocal supporter of the military council since. If the SCAF is bent on pulling the President's constitutional claws, it would be up to Mr Morsi to fight it. And whether or not he did so would determine Egypt's political future.

More than anything, Egypt needs a leader who can start to unify its fractured society and address its increasingly acute economic problems. The optimism of February 2011 is not entirely spent, but there is much cause for concern. Tahrir Square may see more protests yet.