Hours after the official results are announced in Egypt’s first-ever competitive presidential election, Ihab Badawi, a 28-year-old lawyer, is standing amid a throng of protesters in Tahrir Square. He holds aloft a cardboard placard bearing the smiling faces of the top two candidates—Mohamed Morsi and Ahmed Shafik—crossed out with a pair thick black Xs. Traffic snarls around the crowd as he echoes chants rising above the cacophony of angry car horns.

“We do not accept this outcome,” Badwai says. “We are here to send a clear message to the military council and the rest of the corrupt ruling regime: the Egyptian people will not be silent.”

Less than two miles away, a group of protesters breaks into and vandalizes Shafik’s campaign headquarters in the residential district of Dokki before setting it ablaze. Demonstrations erupt in other cities across the country, including Alexandria, Port Said, Ismailia and Suez.

In the wake of the first round of Egypt’s landmark presidential election, the country is as polarized as ever, with two candidates sitting on opposite poles of a divide that has characterized Egyptian politics for decades.

Some 23 million Egyptians cast ballots in last week’s poll, a turnout of 46 percent. Morsi, the Muslim Brotherhood’s candidate, came in first out of thirteen candidates with 24.3 percent, followed closely by Shafik, Hosni Mubarak’s last prime minister, with 23.3 percent. The two will face each other in a June 16–17 runoff to become the first democratically elected president in Egypt’s history.

Yet neither man is considered a revolutionary candidate; one representing a decades-old conservative Islamist opposition group, the other with strong ties to Mubarak, who was ousted in a popular uprising fifteen months ago.

“A substantial number of people who are ‘pro-revolution’ had hoped for an outcome that wouldn’t be this binary choice that Hosni Mubarak had warned of for so long: if it’s not him, it’s the Muslim Brotherhood,” says Issandr El Amrani, a Cairo-based political analyst. “A lot of people were hoping for a wider opening.”

While the result may be a deeply divisive one, the bulk of the votes in the first round— nearly 40 percent—went to candidates considered to be in the spirit of the revolution. Hamdeen Sabahi, a Nasserist socialist, two-time member of parliament and longtime dissident who was jailed seventeen times under successive presidents, surprised many by coming in at third place with a dark horse candidacy that captured 20.4 percent of the votes. Abdel Moneim Aboul Fotouh, a liberal Islamist and former Brotherhood member who ran a “big tent” campaign that garnered supporters ranging from secular liberals to ultraconservative Salafis, came in fourth, with 17.2 percent.

Amr Moussa, the former Arab League Secretary General and former foreign minister under Mubarak who was long considered the front-runner in the race, came in at a distant fifth place with 10.9 percent.

While the vote was considered the freest and most transparent in decades, serious allegations of fraud have been put forward. Sabahi and Aboul Fotouh both filed appeals to the presidential election commission claiming violations in the poll, including allegations of bribes for votes and that police and military conscripts illegally cast ballots. Shafik also filed an appeal saying that votes cast for him in one province were not included in the ballot count. All appeals were quickly rejected by the presidential elections commission with little explanation. The commission’s decisions are immune from any challenge or appeal.

The Carter Center, one of three international organizations accredited to witness the election, said it was only able to conduct a “limited mission,” with monitors receiving credentials less than a week before the vote. Monitors were also prevented access to the final aggregation of results. Yet the group said the vote was generally acceptable and that the irregularities wouldn’t have an impact on the final results.

“We have had restraints placed on us as witnesses that have never been present before,” says former US President Jimmy Carter, who led the mission. “There is no way we can certify that the entire process has been proper. But what we’ve observed, I would say, has been encouraging to me.”

Shafik’s controversial candidacy and second-place finish in the first round of the presidential race sent shockwaves through Egypt’s body politic, which had dismissed him as too counter-revolutionary. A retired general who once commanded the country’s air force, he is widely viewed as the favored candidate of the Supreme Council of Armed Forces that has ruled the country since Mubarak’s ouster. He served as Mubarak’s civil aviation minister for ten years—before being named prime minister on January 29, 2011, four days after the revolution began. The notorious “battle of the camel”—when regime thugs invaded Tahrir on horseback and camel—took place during his tenure, as did the widespread arrests of journalists and protesters. He was forced out of office three weeks after Mubarak’s overthrow amid sweeping protests against him. Since then he has made several provocative statements praising Mubarak and expressing sorrow over the revolution.

In the race for the presidency, Shafik has campaigned on a law-and-order platform, vowing to use brutal force to restore security within a month and to act as a bulwark against the rise of Islamists in government.

“He speaks the language of Mubarak’s regime,” says Heba Morayef, the Middle East and North Africa researcher at Human Rights Watch. “What that means is the retention of broad discretionary powers given to the executive and security forces and a very strong role for security agency involvement to ensure stability and control over protests, which, as far as he is concerned, are the source of instability.”

Shafik’s tough talk appears to have resonated with a large segment of the electorate, yet experts believe his success in the election also relied on robust institutional backing.

“There still remain patronage networks that we didn’t see at work in the parliamentary elections, where the old NDP—the former ruling party—networks, did not perform well,” El Amrani says. “But they seem to have come back with a vengeance in this election.”

Serious questions also remain about the very eligibility of Shafik’s candidacy. Last month, the Muslim Brotherhood–dominated parliament passed a law to ban former senior members of the Mubarak regime from running for president for ten years. The law initially targeted Omar Suleiman, Mubarak’s former intelligence chief and his first and only vice president, but also applied to Shafik. However, the presidential election commission accepted an appeal by Shafik and allowed him to run, referring the case to the Supreme Constitutional Court, which is due to issue a ruling on June 11.

Voters who did not support either Shafik or Morsi in the first round now find themselves facing a painful dilemma in the runoff: forced to choose between a former stalwart of Mubarak’s regime or a member of the Muslim Brotherhood, an Islamist group that already controls the legislature and which is widely viewed as having abandoned the revolution over much of the transitional period in pursuit of its own agenda.

The Muslim Brotherhood demonstrated an unparalleled ability to mobilize its base through a vast grassroots network, organizational structure and discipline within its ranks, delivering 24 percent of the vote for Mosri, the president of its Freedom and Justice Party. Yet the election result represents a significant drop in support from the 47 percent the group captured in parliamentary elections last fall.

“The reason for that drop has been the perception, widespread among all of the revolutionary segments, that the Muslim Brotherhood has really just been looking out for its own interests,” says Abdullah Al-Arian, an assistant professor at Wayne State University who was closely studied the group. “At certain times, when it suited the movement and its political wing, it has cooperated with the SCAF government at the expense of the revolutionaries.”

In parliament, Brotherhood members have been criticized for not pushing a reform agenda. Its MPs have argued in favor of retaining criminal penalties of up to ten years for failing to obtain a permit to demonstrate, proposed a draft law on trade unions that is widely viewed as repressive, and helped pass critical amendments to the Code of Military Justice allowing the military to keep trying civilians in military courts—a practice that ranks among the top human rights violations in post-Mubarak Egypt. More broadly, in the wake of repeated crackdowns on protesters by security forces, “the Brotherhood did not appear interested in seeking accountability for excessive use of force used by the army and Ministry of Interior,” says Morayef.

The Brotherhood has also engendered a deep mistrust among liberal political forces for reversing its earlier pledge not to field a presidential candidate and for going back on its promise to only contest 30 percent of seats in parliament. Most egregiously, the Brotherhood sought to dominate the formation of the Constituent Assembly in April by stacking the body with many of its own parliamentarians and other Islamists or their sympathizers. The move prompted a mass walkout by liberal parties, union representatives, constitutional judges, the Coptic Church and Al-Azhar, forcing the collapse of the body. Negotiations over the constituent assembly have remained deadlocked ever since.

“Had the Muslim Brotherhood been running against another revolutionary candidate—like Sabahi or Aboul Fotouh—I don’t think they would stand much of a chance in the runoff,” Al Arian says. “Their only hope right now is to convince the Egyptian people that they’re actually the much better alternative to the idea of returning back to the Mubarak era, which is what Shafik effectively represents.”

Both candidates are now looking to capture some of the 40 percent of the vote that went to Aboul Fotouh and Sabahi by alternatively offering concessions to outside political forces in the form of vice presidency posts, a coalition government and promises on the formation of the constituent assembly, but concrete deals have yet to be struck.

Casting a long shadow of ambiguity over the entire election process is the fact that voters in Egypt are electing a president without a clear idea of what authority he will actually have vis-à-vis the military, the parliament and the other branches of state. Few expect the military council to hand over full executive authority to the elected president on July 1 without retaining some powers in order to protect its political and economic interests. Some believe the military council will tailor amendments to the constitutional declaration depending on who wins the race.

“The constitutional and institutional and legal framework of the entire transition has been very flawed,” says El Amrani. “I think the critique of someone like Mohamed El Baradei, who refused to run for the presidency precisely because he thought the framework wasn’t sound, was valid.”

As divisions deepen over whom to vote for in the runoff, activists have begun advocating a third alternative: a boycott. Pointing to real questions over the validity of the entire process as conducted under military rule and the widespread disenchantment over the lesser-of-two-evils choice between Shafik and Morsi, some segments of the revolutionary youth are actively calling for voters to boycott the runoff in order to depress the low first round turnout of 46 percent to such a degree so as to throw into question the popular legitimacy of the elected president.

“Elections are the graveyard of revolution,” says Rasha Azab, a prominent activist and protester who boycotted the first round the presidential elections and is boycotting the runoff. “The regime still exists and is using all of its tools, the only thing that happened is, they will change from Mubarak to Shafik or Morsi.”