TO the dismay of every Egyptian who hoped the Arab Spring of 2011 would herald a decisive new beginning, the outcome of last week's historic presidential election looks almost certain to produce a run-off between a conservative Islamist backed by the Muslim Brotherhood and a former air force commander with close links to the former administration of disgraced president, Hosni Mubarak.

Although the actual result will not be known until this Tuesday, the count has been completed in 90% of the country's 13,000 voting stations, and everything points to a confrontation in mid-June between Mohamed Mursi, the Muslim Brotherhood candidate and Ahmed Shafiq, who served briefly as prime minister in the final days of Mubarak's rule.

There is still an outside chance that Shafiq will lose out to the former head of the Arab League, Amr Moussa, who has called on his rival to stand aside, but if a Mursi-Shafiq contest is the upshot of the election it will come as a disappointment to those who yearned for the emergence of a democratic and secular Egypt based on religious and social tolerance.

When the two politicians do go head-to-head for the presidency they will offer the Egyptian people a choice between the strict Islamic values of the Muslim Brotherhood and a perpetuation of the role of the armed forces in the country's politics. At the same time the two "candidates of the revolution", the liberal Abdel Moneim Aboul Fotouh and the socialist Hamdeen Sabahi, will probably finish poorly in third or fourth place.

Their failure to make any impression on the electorate shows how polarised the country has become in the aftermath of Mubarak's fall from power last year. In that time the country has been fractured politically and economically and all political power has been controlled by the Supreme Council of the Armed Forces, which represents the only continuation of authority.

The generals have promised to step aside at the end of June once a new president has been elected but most Egyptians remain deeply suspicious of the influence wielded by the armed forces, and with good reason – the army has controlled Egyptian politics for 60 years.

Everything points to a drastic rise in the political temperature when the competition between Mursi and Shafiq begins in earnest, as both men carry substantial amounts of baggage. As a member of the previous regime and a senior officer, Shafiq might represent a sense of continuity, the main reason why his vote was so high in conservative rural areas, but his links to Mubarak fuel suspicions that the military will be pulling the strings.

Mursi, too, has form. A US-trained academic, he lacks charisma and only got the nomination because the frontrunner, multi-millionaire Khairat al-Shater, was disqualified after admitting to a term spent in prison.

Many expect that he will only be a figurehead leader, one who was only be able to contest the presidency because he is backed by the Muslim Brotherhood's formidable electoral machine. Not for nothing has he been derided as the "spare tyre".

And yet, in spite of the result and despite the expected clash between the rival claims of the Islamists and the armed forces, the election has helped to lance a boil in Egyptian politics. After years of living in what was little better than a benign dictatorship, the people of Egypt embraced democratic principles and voted in larger numbers than expected. It was also a relatively good-natured affair, with very few instances of violence or corruption reported, and there was, too, a sense of destiny being fulfilled.

Ahead, though, lie the really tough choices. Mursi seems certain to bring in the Muslim Brotherhood vote, while his opponent will almost certainly be a centrist, perhaps even a military man. That means that Egyptians will be left with the choice of voting for Mursi and the probable introduction of Sharia law and a stricter interpretation of Islam, or for a candidate who will almost certainly have a history which links him to the old order.

Whichever candidate wins, it will send a powerful message to the rest of the Middle East about the direction being taken by the Arab Spring – back towards business as usual or forwards towards the creation of a new Islamic state.