Egypt’s January 25 Revolution last year was supposed to dispel Hosni Mubarak’s false dichotomy: the choice, he often warned, was between his regime and the Muslim Brotherhood. Sixteen months after Mubarak relinquished power, that is still the choice Egyptians will make when voting for his successor.

Last week, Egyptians voted in the freest and fairest presidential election in the history of the Arab world. The process was new, but the interests of the voters were not. Of the two candidates that received the most votes, those who will go head to head in a June 16–17 run-off, one hails from the country’s most established Islamist opposition organization—and post-Mubarak Egypt’s most powerful political group—and the other from the ancien régime of patronage networks and military dominance struggling to maintain its position in a new Egypt.

Mohamed Morsi, chief of the Muslim Brotherhood’s Freedom and Justice Party (FJP), has promised that Egypt will be ruled by sharia, Islamic law. Ahmed Shafik, a former air-force commander and the last prime minister under Mubarak—who allegedly referred to Shafik as his “third son”—campaigned on restoring law and order and countering the rise of Egypt’s Islamists. On Monday, the Presidential Election Commission (PEC) announced these two candidates, of thirteen in the race, garnered just under half the votes, with Morsi coming out slightly more than a percentage point ahead.

Egypt’s two remaining presidential candidates secured their bases in the first round and will attempt to court the supporters of other candidates with more centrist positions. Both Morsi and Shafik used victory press conferences to appeal to revolutionaries: Morsi said a vote for him is a vote to protect the revolution; Shafik announced he shares the revolution’s goals of “bread, freedom and social justice.”

Despite this posturing, many analysts and at least one opposition party have called the Shafik-Morsi showdown the “worst-case scenario.” For eighteen days in early 2011, the world watched as Egyptians in Tahrir Square challenged and later toppled President Mubarak in the name of democracy. With a presidential runoff between Morsi and Shafik, where does the prospect of a successful democratic transition in Egypt stand?

Shafik is the epitome of the old regime, with its intolerance of dissent, heavy-handed security forces and crony capitalism. Omar Ashour, a visiting fellow at the Brookings Doha Center, told CNN that Shafik could not win without vote rigging and that his election as president could result in a second revolution. Given that Shafik campaigns as the “law-and-order” candidate, his election very likely could result in a violent clash between protesters and security forces. The very evening Shafik’s second-place finish was confirmed, his campaign’s Cairo headquarters was ransacked.

Morsi has the Islamist vote, probably Egypt’s largest constituency, in his favor. If Shafik wins, this will play into Al Qaeda’s narrative—a narrative that until now has been largely rejected in Egypt—that Islamist gains cannot be achieved without violence. Thanks to the Libyan revolution and years of smuggling in the Sinai, Egypt is awash in weaponry if its former jihadis decide to return to their terror-filled insurgency of the 1980s and 1990s.

The flip side of the scenario is Morsi: a man beholden to his oath to the supreme guide of the Muslim Brotherhood over any oath to his nation. President Morsi, who would appoint a prime minister and government, would have the support of the Brotherhood’s FJP and its plurality in both houses of parliament to enact any policy he and the Brotherhood want. Khalil Anani, an Islamist expert at Durham University, noted on Twitter that this “will create a new tyranny,” especially because the non-Islamist opposition is so weak and divided.

Several possible surprises hang over the presidential election’s milestone toward democracy. The PEC rejected all appeals of irregularities and vote rigging, but independent Islamist candidate Abdel Moneim Aboul Fotouh has demanded that elections be stalled until the so-called “disenfranchisement law” is settled. Indeed, the law banning Mubarak-era figures from elected office all but targeted Shafik by name. The Supreme Constitutional Court is reserving judgment on whether or not the law is “constitutional” until at least late June, which puts Egypt in the awkward position of possibly electing a president who is immediately disqualified from serving.

Of course, what is unconstitutional today may be different tomorrow. Most disturbing about the possible FJP sweep of Egyptian political leadership is that Egypt’s new constitution has yet to be written; tellingly, the drafting process was disrupted when the Brotherhood attempted to monopolize the Constituent Assembly. If Shafik wins the presidency, the Brotherhood can check his power through the parliament, not to mention a new constitution that could leave the president powerless. Such a balance of power would not exist if Morsi wins. However, the Brotherhood only decided to run a presidential candidate because of another threat: President Shafik, or the judiciary loyal to the old regime, could dissolve the parliament, leaving the Brotherhood—and the entire opposition—without its electoral legitimacy.

These factors would be enough to consider in a normal democratic environment, which certainly Egypt is not. The military has played an overbearing role throughout the sixty-year history of the Egyptian republic, not to mention the heavy-handed actions of the ruling Supreme Council of the Armed Forces (SCAF) since the revolution. In reality, the Brotherhood could not run the political tables if it gained the presidency because Morsi and his government would still have to contend with the military. Since the revolution, the Brotherhood has only challenged the military up to a point before backing down. Brotherhood leaders have a long memory. They recall that the last time they colluded with the military was in 1954, when Gamal Abdel Nasser crushed the movement after they were no longer useful. The Brotherhood may think this is its chance for revenge, but the Algerian election of 1991 and the Palestinian election of 2006—both of which were followed by an increase in internal hostilities—sit heavy on the minds of Brotherhood leaders.

The SCAF has shown over and over that it has no interest in giving up military prerogatives. As such, a contest between the military and the Brotherhood will continue to simmer. Egyptian voters must decide if they prefer that conflict out in the open or behind the scenes. A Shafik presidency could block the independent parliament’s ambitions on behalf of the military, and a President Morsi would always have the possibility of a coup in the back of his mind. Neither scenario is particularly democratic.

Zack Gold is a Washington-based Middle East analyst. Follow him on Twitter:@ZLGold