Results from Sunday's presidential run-off election will not be confirmed until 21 June, but if Egypt's first democratically elected president is Muhammed Mursi, the Muslim Brotherhood candidate, this would represent the most significant break with the Mubarak regime. It would also be a major step towards the consolidation of the Arab Spring.
However, this major development has been overshadowed by the Supreme Council of the Armed Forces' (SCAF) declaration, as polls closed, to give itself sweeping legislative and budgetary powers. This includes the mandate to initiate legislation, to appoint a panel to draft the constitution, to control it's own budget, and strip the presidency of power over the military.
This is a desperate attempt by SCAF to maintain a hold on power and to protect it's own position, in the event of Mursi becoming president. This is despite attempts to manipulate the presidential race through it's presidential candidate, Ahmed Shafik, Hosni Mubarak's last prime minister.
SCAF is trying to stack as many cards in it's favour as possible before abiding by its promise to hand over power on 30 June. The public prosecutor gave instructions to stop the implementation of the Emergency Law on 31 May, which had been enforced since 1981. But within days a new decree through the Justice Ministry granted military police and intelligence officers the right to investigate and arrest citizens for a wide range of offences.
When voting for the presidential run-off got underway, SCAF issued amendments to the Constitutional Declaration to limit the powers of the President and increase those of the military. Among the articles amended is Article 60, giving SCAF authority to veto provisions that 'conflict with the goals of the revolution or good of the nation'.
Two days before voting began, Egypt's Supreme Constitutional Court passed a verdict, reached by judges appointed under former President Mubarak, dissolving the country's elected parliament, which was dominated by Islamists. The court ruled that last year's parliamentary polls were unconstitutional because they had allowed party members to vote for seats reserved for independents in the Lower House. This assertion of SCAF's power through the judiciary undermines the independence of yet one more arm of the state and puts into question the prospects of Egypt's transition to a civilian state.
SCAF has systematically tried to rob the parliamentary elections of legitimacy, partly conducted through a concerted state media campaign against the Freedom and Justice Party (FJP) and the Islamists in general. Egypt's deteriorating economic situation, the biting fuel shortages, and the overall ineptitude of the SCAF backed Ganzouri government has increased public anger and frustration. The Islamist parliamentarians have borne the brunt of the anger, after high expectations they would deliver. However there is little they could do when not in government . Furthermore, SCAF's interests were served as the FJP became increasingly mired in the political debate about the makeup of the constituent assembly which drew increasing opposition because it was seen as Islamist dominated.
The failure by secular and liberal forces to vigorously oppose the dissolution of parliament and the acquiescence and even approval of some of those forces because of their dislike of having an Islamist dominated parliament has far reaching implications for the commitment to, and progress, of parliamentary politics in Egypt.
Egypt is facing the greatest challenge to the uprising of January 2011 against President Mubarak.
Since then, SCAF has expanded its powers and as such, for those among the many of the public who chose to boycott the elections, either presidential candidate winning is seemingly irrelevant. However, having Shafiq in power would make SCAF's task easier and ensure the protection of remnants of the old regime - and of the state it fostered with it's security apparatus, even if cosmetically reformed.
In Muhammed Mursi, Egypt would likely have a president who along with his supporters have suffered from a repressive dictatorial system for decades, which was backed by the military and which they want to dismantle, even if this will have to be done gradually, and with limited powers.
SCAF wants to ensure it ultimately remains in control, which renders the political and security situation extremely volatile. If it feels increasingly threatened, SCAF will resort to more repressive measures to ensure it's own protection.
For Mursi and his supporters, the situation is fragile. The presidency allows them a lever of power despite enormous challenges. Although, a Mursi victory would be limited by SCAF, it would nevertheless be an endorsement of the Arab Spring, although it's goals might take longer to achieve than was hoped.
For the US and the EU now is an opportunity to show their commitment to democratization in the region by using their leverage to help the transition to a civil state.
Dr Maha Azzam is Associate Fellow in the Middle East and North Africa Programme.