Egypt

Cairo (CNN) -- As Egyptians cast ballots Sunday in the second and final day of a runoff that will decide the country's first popularly elected leader, questions swirled about whether the military would actually relinquish power.

The runoff was taking place against a backdrop of political confusion: Egypt has no constitution and no parliament, following a court ruling just days before the runoff that invalidated an Islamist-dominated legislative body and then saw the military swiftly move to dissolve it ahead of the election.

Even the choice of candidates in the runoff appeared to reflect the political polarization spurred by the chaos: Mohamed Morsi, backed by the once-banned Muslim Brotherhood, and Ahmed Shafik, who served as the last prime minister in the waning days of Hosni Mubarak's regime.

The two-day runoff that began Saturday followed a May election that failed to produce a winner with a clear mandate.

Polls opened again at 8 a.m. (2 a.m. ET) Sunday. They were scheduled to be open until 10 p.m. after election officials extended voting for two hours. Votes must be counted by Monday, with finals results to be announced Thursday.

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Turnout appeared sluggish Sunday at some polling stations in Cairo. Some voters may have stayed home because of sweltering heat, officials told the state-run Al-Ahram newspaper.

As of 4 p.m. Sunday, 40% of Egypt's 50 million eligible voters had cast ballots nationwide, said Farouk Sultan, head of Egypt's Presidential Election Committee. In the first round of voting last month, 46% of voters participated.

Officials have reported few voting irregularities in the second round of elections, Sultan said.

The streets in Cairo were mostly quiet during balloting despite what many Egyptians viewed as a move by the Supreme Council of the Armed Forces, which has ruled the country since Mubarak was forced out in February 2011, to hold on to power.

Outside the city, in Giza, Mohammed Gamea cast his ballot for Morsi even as he questioned whether the election was fairly handled.

"I don't believe the Egyptian presidential elections are fair to begin with," he said Sunday morning. "The military council, assisted by the elections committee, tried everything to stall and influence the process, from disqualifying previous candidates before the first round -- not to mention the negative campaigns against Morsi -- while keeping quiet about Shafik."

"But despite all, I don't believe that there has been any electoral fraud. The ballots will determine what is next for Egypt."

The ballots in Egypt feature not only the names candidates but their pictures as well.

To protect the balloting process, authorities have gone so far as to camp outside polling stations overnight during the runoff. At one station designated for women in Cairo, guards slept on the doorstep.

The Supreme Presidential Electoral Commission approved licenses for 53 organizations to observe the elections, including at least three international groups -- the U.S.-based Carter Center, the South Africa-based Electoral Institute for Sustainable Democracy in Africa and the Arab Network for Monitoring of Elections.

Meanwhile, the April 6 youth movement, which was behind many of the protests in Cairo's Tahrir Square last year, said 36 members were arrested during protests Saturday, but most were released by that night.

Some disgruntled voters launched a campaign to invalidate ballots, said Mohamed Ghoneim, the founder of a group that marked "X" on the names of both Morsi and Shafik, thereby nullifying their vote.

Among the boycotters was Mohamed Khamees, who handed out leaflets.

Khamees said he lost sight in his left eye from a police beating in Tahrir Square during the early 2011 protests.

"If I give this country for the Brotherhood hands, there is not going to be any more Egypt, it will be destroyed," he told CNN. "And if I give it to someone from the old system, it looks like we did nothing."

There are a number of questions about what happens after the election.

Following the move to dissolve parliament, the military council said it will announce a 100-person assembly to draw up a new constitution.

In the meantime, though, the military council also said it is drawing up an interim constitution that will lay out the powers of the new president -- a move not expected until after the elections.

That's a result that sits uncomfortable with many of Egypt's voters.

The Muslim Brotherhood called for a referendum, saying the dissolution of parliament a dangerous step taken by the military.

"We are calling for a referendum again on the dissolving of parliament and see it as the logical thing to do especially after 30 million people went to the polls the first time and the country spent over 3 billion Egyptian pounds in a transparent electoral process," said Mahmoud Ghozlan, spokesman for the Brotherhood.