But only Friday morning did it appear that second place would go to Ahmed Shafik, a former Air Force general who briefly served as Mr. Mubarak’s last prime minister. A late entry into the race, Mr. Shafik was a dark horse campaigning on promises to use a firm hand against the protests and lawlessness that have prevailed since Mr. Mubarak’s ouster. He presented himself as a strong check on the rise of the Islamists. Of all the candidates in the race, Mr. Shafik came closest to promising a restoration of the old order and aroused vocal support and threats of a “second revolution” if he should win.
Mr. Shafik’s law-and-order message resonated with voters, helping him to overtake the two candidates previously considered, along with Mr. Morsi, to be the front-runners. One was Amr Moussa, a former foreign minister under Mr. Mubarak and former head of the Arab League, who had offered a softer but similar message. In the final weeks of the race, Mr. Moussa’s support appears to have all but collapsed in favor of Mr. Shafik.
Ahmad Sarhan, a spokesman for Mr. Shafik, said voters had rallied to the candidate because he promised to “save Egypt from the dark forces,” referring to the Brotherhood and more militant Islamists.
Mr. Shafik would bring back security, Mr. Sarhan said. “The revolution has ended,” he said. “It is one and a half years.” The other former front-runner who fell behind Mr. Shafik was Abdel Moneim Aboul Fotouh, a dissident former Brotherhood leader campaigning as an Islamist and a liberal. Mr. Aboul Fotouh explicitly challenged the Brotherhood’s authority to speak as the voice of political Islam. His iconoclastic campaign promised to upend the old culture-war dichotomies of Egyptian and Arab politics, and it caught fire among an unlikely alliance of Brotherhood youth, ultraconservative Islamists known as salafis, and more secular-minded leftists and liberals.
But in the final weeks of the campaign, some of his more secular-minded supporters appear to have shifted their allegiance to another dark horse, Hamdeen Sabahi, a Nasserite socialist. Mr. Sabahi and Mr. Aboul Fotouh trailed Mr. Shafik with almost all the votes counted, but the tally was not yet final.
Some liberals and leftists had argued that, in a country where 75 percent of the parliamentary vote went to the Brotherhood or more conservative Islamists, Mr. Aboul Fotouh was their best hope to challenge the Brotherhood’s political dominance. But after Mr. Aboul Fotouh accepted the endorsement from the main party of the ultraconservative salafis a few weeks ago, some high-profile artists and intellectuals jumped to Mr. Sabahi.
Mr. Sabahi offered an alternative for those who opposed the Islamists and the former Mubarak government. A former poet turned populist, he combined a history of opposition to Mr. Mubarak, a public embrace of the arts, and full-throated defense of the cause of workers and farmers. He promised heavy taxes on the rich, more subsidies for the poor, a greater state role in the economy, and an end to the “the spirit” of Egypt’s Camp David peace treaty with Israel.
As the votes were counted Friday morning, some liberals and leftists ruefully observed that, taken together, Mr. Aboul Fotouh and Mr. Sabahi attracted more votes than Mr. Shafik or Mr. Morsi. Neither, however, will enter the runoff.
Mr. Morsi’s success was itself a testament to the depth of the organization’s grass-roots network and popular appeal, which may make him hard to beat in the runoff.
He was widely regarded as the least charismatic of the leading candidates. He was derided as a mere “spare tire” who was pulled in after the disqualification of the Brotherhood’s first choice, of its leading strategist, Khairat el-Shater. Mr. Morsi mainly promised to execute Mr. Shater’s plans and platform, and Mr. Morsi’s own face barely appeared in his two television commercials. He did not participate in the single televised debate, in which Mr. Moussa faced Mr. Aboul Fotouh.
But his victory also came at a political price. To fend off the Islamist-versus-Islamist challenge from Mr. Aboul Fotouh, Mr. Morsi and the Brotherhood dropped some of their efforts to cultivate a moderate image and turned their campaign appeals sharply to the right.
After distancing itself from the more conservative salafis during and after the parliamentary voting, Mr. Morsi and the Brotherhood embraced them on the campaign trail, eagerly standing with them. He called himself the only true Islamists in the race, led chants for the implementation of Islamic law, and portrayed his political program as a distillation of Islam itself.
Some of those shifts may now complicate the group’s efforts to project a more moderate, centrist image, in the runoff and in its dealings with the West as Egypt’s dominant political force.
“We are in the lead,” Essam el-Erian, a leading Brotherhood lawmaker, said at a midnight news conference. “God willing, Mohamed Morsi will be the next president of Egypt.”
Egypt’s Christian minority, which makes up about 10 percent of the population, rallied around Mr. Shafik in a coordinated effort to vote as a bloc against the Islamists, voters and Christian leaders said.
“Because of his military background, Copts are confident he will be strong enough to restore security and enforce the rule of law,” said Youssef Sidhom, the editor of Watany, a Christian newspaper. A committee of lay political leaders had convened about six months ago to devise a Christian strategy for the presidential vote, Mr. Sidhom said. “After much hesitation between Moussa and Shafik, the final word was Shafik, in order to avoid splintering the Coptic vote.”
Fears of the Islamists appeared to have outweighed any reluctance by Christians to support a candidate from the military, despite the killings of dozens of Christian demonstrators by soldiers just a few months ago. After the massacre, senior generals sought to blame the Christian demonstrators for scaring the heavily armed troops.
Mr. Sidhom said Coptic leaders had concluded, however, that there was no military “conspiracy” against the Copts that resulted in the massacre. “There was a kind of chaos and panic among the small number of troops who were stationed there,” he said, although he noted that there had been no criminal investigation.
Officials of the Brotherhood, who have the best national organization of poll watchers, said more than half of the 50 million eligible voters turned out to vote on Wednesday and Thursday. Journalists and other nonpartisan observers reported orderly lines and no evidence of systematic abuses. At 9 p.m. on Thursday, the polls closed and ballot counting started in each polling place, in the presence of observers from the campaigns and monitoring groups.
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Reporting was contributed by Kareem Fahim, Dina Salah Amer and Mayy el Sheikh. The New York Times