Once again Egyptians find themselves facing the unknown. The result of the first round of presidential election was inconclusive and a run-off vote will take place in three weeks’ time to determine who becomes the country’s first freely elected president. But even then Egyptians will remain polarised. Now they have to choose between two candidates who may chart two divergent futures for the country.

The choice will not be easy for the majority of voters. Last week’s election, described as the freest in the country’s history, showed that secular candidates received more than 50 per cent of the votes, but Mohammad Mursi of the Muslim Brotherhood came in first, with about 25 per cent — in contrast to the 40 per cent the movement’s candidates won in parliamentary elections last January.

The biggest surprise was the unexpected rise of independent candidate and last prime minister under president Hosni Mubarak, retired Gen. Ahmad Shafiq. He came in second after winning 24 per cent of the votes. His success represented a defeat of the forces of the 25 January revolution which toppled Mubarak last year.

Shafiq’s opponents describe him as a feloul; a remnant of the old regime. His success has baffled observers and left many Egyptians bewildered.

Other candidates, who were supposed to do well, like former secretary general of the Arab League Amr Musa and independent Islamist Abdul Moneim Abofotouh, performed badly.

Socialist candidate Hamdeen Sabahy’s miraculous feat at the polls — he came in third place — underlined the fact that millions of Egyptians believe there is a third choice.

Until the run-off vote between Mursi, of the Freedom and Justice Party (FJP), and Shafiq takes place in June, the two candidates will attempt to appease the large and critical mass of voters who remains on the sidelines.

The Islamists know that their popularity in the street has been reduced, largely due to the poor and chaotic performance of the Muslim Brotherhood leadership and its candidates in parliament.

Morsi vowed to open up to all political forces, including the secular youth who insist on a civil state. On the other hand, Shafiq distanced himself from the old regime, and promised to reclaim the hijacked revolution and hand it over to its rightful owners.

Earlier attempts by Mursi to woo Sabahy and Abofotouh were unsuccessful. And it is unlikely that Shafiq will be endorsed by major political players.

Still his chances in the second round are not slim. He will rely on the important Coptic vote and on the fact that many middle-class Egyptians would not want to see their country governed by an Islamist president who believes in a Sharia-ruled state.

Shafiq may still be able to mobilise the voters who opted to stay home last week, while Mursi will depend on the efficiency of the brotherhood’s voting structure. It is likely that many Salafists, who were backing Abofotouh, will now support him in the second round.

This uncertainty is new to Egypt. Previous presidential elections were characterised by fraud and corruption. Now, and in spite of the uncertainty about the future, Egyptians are celebrating their nascent democracy. Their choice in the runoff will be historic and will have a dramatic effect on the entire region.

Despite the surprises, the current showdown makes a lot of sense. The first republic was born out of close collaboration between the Muslim Brotherhood and the Free Officers movement, led by Gamal Abdel Nasser, which overthrew the monarchy in 1952. But that partnership was short lived. Nasser rejected the brotherhood’s political programme and, in 1954, banned the movement and waged war against it.

Today, the second republic is facing the same difficult choice that was put on hold for six decades. But the Arab Spring has altered the rules of the game.

Egypt’s woes will not be over after a new president is elected. Mursi’s success will bring parliament and the presidency under the Muslim Brotherhood’s control. Many Egyptians are worried that such concentration of power will recreate the ruling party saga of the last 30 years.

There are no guarantees that the Islamists will honour their promises to maintain a civil state and protect the rights of women and minorities. And they are bound to have a direct effect on the nature of the new constitution, which will outline the president’s authorities.

On the other hand, if Shafiq wins the day, the revolution may erupt again. His victory will drive many of Egypt’s frustrated youth back to Al Tahrir Square, while he will face a hostile legislature.

One political activist, George Ishaq, said the results of the first round have placed Egyptians between the hammer and the anvil.

On Twitter, Egyptian activists reacted to last week’s events. One asked: “Did we sacrifice 1,000 martyrs to get rid of the old system only to see a Mubarak loyalist score such a big victory?”

A Shafiq supporter had this to say: “The revolution brought havoc and Shafiq will restore law and order and bring stability.”

Many Egyptians have grown tired and frustrated over the past year. They want to see a strong man at the helm, someone who can salvage the economy and stop the Islamist tide.

It is ironic that for years Mubarak rejected calls for reforms, saying that it was either him or the Islamists. Now that he is gone, it appears he was right.

The writer is a journalist and political commentator based in Amman.