MADRID – As Egyptians tensely awaited the results of their country’s presidential elections, a thread of pessimism ran through the discourse of the young people and secular liberals who had brought down Hosni Mubarak in January 2011. The “anything is possible” sensation of the Tahrir Square rebellion had faded, and now two candidates whom the protesters deeply opposed, the Muslim Brotherhood’s Mohamed Morsi, and Ahmed Shafiq, a factotum of the old regime (and of the current military government), prepared to face off in the second round.

The triad of fundamental forces driving Egypt since the beginning of the Arab Spring – the military, the mosque, and the masses in Tahrir Square, each with different types of power and interests – was thus broken. Those who filled Tahrir Square 16 months ago were silenced, and the expected transfer of power from the military to a civilian, democratic government was thrown into doubt.

Since assuming power after Mubarak’s fall, the Supreme Council of the Armed Forces (SCAF), led by Field Marshal Mohamed Hussein Tantawi, a defense minister for two decades under Mubarak, has consistently undermined the delicate work of democratic transition. The week before the presidential elections, the SCAF-allied Constitutional Court dissolved the recently elected parliament, alleging illegality in the voting process. And, foreseeing Morsi’s victory, SCAF assumed all legislative powers; severely limited the president’s powers; seized the authority to appoint the committee tasked with drafting the new Constitution; took control of the country’s budget; and claimed sole power over domestic and foreign security.

As a result, Egypt’s power struggle will continue, with the junta no longer battling those in Tahrir Square, but political Islam. After a decades-long clandestine (although tolerated) existence within Egyptian society, Islamist forces were able to take advantage of the Tahrir protests, despite playing no integral part in them. The secular liberal forces’ political fragmentation and lack of organization cost them dearly in the parliamentary elections six months ago, and, in the second round of the presidential election, a majority of Egyptians chose Morsi over a restoration of the old regime.

But Morsi’s narrow margin of victory (just 3.5 percentage points) over Shafiq, and low voter turnout – 46.4% in the first round and 51.8% in the second – reflect a polarized, exhausted society that lacks confidence in the electoral process and the candidates. Moreover, the outcome has merely fueled further uncertainty about Egypt’s direction.

With Morsi’s victory, some now fear that the Muslim Brotherhood will seek to implement radical policies aimed at Islamizing a Muslim country that is already conservative, but that has had a secular government for decades. Others do not believe that the Muslim Brotherhood will go so far, but nonetheless doubt that the Brothers will defend a secular, truly democratic regime in the ongoing negotiations with SCAF on a transition to civilian rule.

In either scenario, Morsi has little room to maneuver in a country that, for the time being, is in political limbo – with neither a constitution nor a parliament – and whose people want tangible results in terms of good governance, institutional consolidation, and improvements to a tottering economy.

Indeed, living standards have been under severe pressure since Mubarak’s downfall. In 2011 alone, net capital inflows fell nearly 90% year on year, tourism was down 30%, the trade deficit soared to $28 billion, and GDP growth slowed from 3.8% to 1%. The success or failure of Morsi’s government will rest largely on the economy.

For the Muslim Brotherhood, this scenario constitutes a serious challenge, one that can be overcome only by finding an adequate balance between SCAF, with its overweening power, and Egypt’s liberal political forces – which won a combined 11 million votes, five million more than Morsi, in the presidential election’s first round. Only this will give a Morsi administration the necessary legitimacy and capacity to carry out a joint transition with the military for a true change of regime.

The liberals, for their part, did not support Morsi in the run-off with Shafiq. But it was their efforts that made the presidential election possible in the first place, and many now believe that close collaboration with the Brothers is the only available option that can restore some of the spirit of an endangered revolution in which they were the protagonists.

This presupposes that the Brothers reorganize themselves internally and find ways to distance themselves from more radical factions, and that they promote inclusive policies toward vulnerable groups and social minorities. For now, the Brothers have announced that they will name a Christian and a woman as Vice Presidents. Obviously, that represents an encouraging first step in bridging Egypt’s divides. But, just as obviously, it is only a first step.

Read more from our "Electing Islam" Focal Point.