The first round of the Egyptian elections produced results with devastating implications for the success of the country’s transition. Mohamed Morsi, the Muslim Brotherhood’s candidate, and Ahmed Shafiq, a former military officer as well as minister and prime minister under Hosni Mubarak, received the highest number of votes. With 24.9 percent of the vote Morsi is slightly ahead of Shafiq who received 24.5 percent, according to unofficial returns.

This was the worst possible outcome of the elections: it is the prelude to the direct confrontation between the old regime and the Muslim Brotherhood that Mubarak warned about and used to justify—and win tacit international acceptance for—his authoritarian policies.

The battle will be fought at the polls in the second round of elections on June 16 and 17, but it will also spill over into the fight over the new constitution, the Supreme Constitutional Court’s decision on whether the election law by which the parliament was elected was constitutional or not, and in more mass demonstrations and street battles that are all too likely to lead to violence.

On one side of the battle will be the military, state institutions including the courts that are still controlled by Mubarak-era personnel, the business community, other people who thrived under the old regime, and ordinary Egyptians who want order restored. On the other side will be the Muslim Brothers, most Islamists, and the Egyptians who rose up in January 2011 and do not want to see the regime they thought they had defeated make a comeback.

Uneasily in the middle will stand over 50 percent of Egyptians who did not vote for either Morsi or Shafiq, but for three candidates that represent, in their own very different fashion, an alternative: Hamdeen Sabahi, a secular, left-of-center candidate who surprised everybody, including possibly himself, by winning 21.1 percent of the vote, surging ahead in the last couple of weeks after being dismissed as a serious candidate earlier; Abdel Moneim Aboul Fotouh, a former leader in the Muslim Brotherhood who was expelled from the organization when he announced his intention to run for the presidency against the wishes of the organization, who won 17.8 percent of the vote; and Amr Moussa, former foreign minister and later secretary general of the Arab League, who garnered 11.3 percent of the vote after being considered a front runner for months. Clearly there are many Egyptians who believe there are better choices than accepting Islamism in the name of change or restoring the old regime in the name of stability.

It is impossible to predict the choice Egyptians who rejected both Morsi and Shafiq will make when these are the only candidates. Both Hamdeen Sabahi and Abdel Moneim Aboul Fotouh initially hinted that they would encourage their followers to vote for Morsi in order to keep the old regime from reasserting itself, but they have since retreated and now say they will not endorse anybody. In any case, there is no way of knowing how voters will respond. This was the first time Egyptians ever voted freely in a presidential election with real choices, so there are no established voting patterns to base predictions.

In any case, the vote by itself will not decide which faction will prevail, because many of the battles will be fought outside the electoral arena. Some are already being fought now. One is the battle over the constitution and the other is the battle over presidential powers. In both, the Supreme Council of the Armed Forces (SCAF) and the institutions of the state, especially the judiciary, are the main players.

According to the constitutional declaration issued by the SCAF after the overthrow of Mubarak, the constitution should be written by a 100-member constituent assembly elected by the parliament. The document, however, inexplicability says nothing whatsoever about the criteria for eligibility or even more paradoxically about whether the constitution needs to be approved by a simple or special majority in this body. When Muslim Brothers and Salafis won the parliamentary elections and, unsurprisingly, elected a constituent assembly that reflected the composition of the parliament, secular parties and other organizations howled in protest, which they are entitled to do in a democratic system. The courts declared the election of the constituent assembly invalid and ordered it suspended—in a decision that they may not have been entitled to make because it appears to have been politically rather than juridically motivated.

As a result, there is no constitution yet and nobody knows how much power the new president will have or how responsibilities will be shared between him and the parliament. The SCAF, expected to step down at the end of June after the president is elected, is now trying to issue a new, last-minute constitutional declaration to define the powers of the president, preempting the decision of the constituent assembly and the prerogatives of the elected parliament to choose who will write the constitution.

The second battle already engaged concerns the validity of the parliamentary elections, and here, too, the weapon chosen by the old regime is the courts. The Supreme Constitutional Court (whose president, not incidentally, is also the head of the presidential election commission) will soon rule whether the election law used in the parliamentary election was constitutional. If it decides it was not, it is possible the court will disband the parliament, depriving the Muslim Brotherhood of the only center of power it, rather than the old regime, controls.

Islamist parties, despite their electoral success, have no institutional or legal weapons in this extra parliamentary battle as institutions other than the parliament are all still controlled by the old regime. Should Ahmed Shafiq win the presidential vote and the court finds the parliament was unconstitutionally elected, Islamists will have lost the battle with the old regime. The question is whether they will accept defeat and regroup to fight another time in the confines of the electoral process, as Islamists did in Turkey, or encourage their supporters to take to the streets. The answer may well depend on what the 50 percent of Egyptians who wanted neither a Muslim Brother or a member of the old regime to be president decide to do.

The coming months will be extremely difficult in Egypt, and the political instability will lead to continuing neglect of economic problems. A great deal rides on the outcome of the presidential election, the court case against the parliament, and the writing of the constitution. In the short run, these are the battles that will determine the winners, and the old regime appears to be better armed, controlling the institutions and the security forces. In the long run, the outcome is much less predictable because the majority of Egyptians have rejected both the Islamist candidate and the one from the old regime.

This is something the Obama administration and Congress need to keep in mind in the coming months as they make the difficult choice of how to react to the crisis in Egypt. Whoever prevails in the short run will only have the true support of a minority and at best a grudging acceptance from another segment of the population. The outcome of these particular battles, like the outcome of the battle to oust Mubarak, will not be definitive, but part of a long war. It would be unwise for the United States to take sides now.