In all likelihood, Egypt's new draft constitution, rushed through an Islamist-dominated assembly last month and facing a national referendum this Saturday and next, will be ratified. Once this happens, President Mohammed Morsi, the Muslim Brotherhood leader elected in April, will have legitimacy and the ballot on his side.

That the protesters of Tahrir Square never thought their exertions would end in the ascendancy of the Muslim Brotherhood is a familiar tale in the annals of revolutions. The world over, revolutionaries tell of rebellions hijacked, stolen or betrayed.

Those 18 magical days of protests that culminated in the overthrow of Hosni Mubarak on Feb. 11, 2011, were not meant to bring the Muslim Brotherhood to power. In truth, the Brotherhood's rivals—assorted leftists, secularists, political figures who feuded among themselves—had not been blameless. Released from the quiescence of an entrenched autocracy, they set the stage for a presidential contest that came down to a choice between the Brotherhood and the feloul (remnants) of the Mubarak regime.

In retrospect, it had been idle to hope that the Brotherhood would read its narrow margin of victory in the presidential election as a warrant for caution and restraint. A movement born in intrigue and conspiracy that labored in the shadows for some eight decades, that knew prisons and torture under political regimes of every stripe, was fated to overreach.

The Brotherhood had never known a genuinely revolutionary tradition: From its rise in the late 1920s, its politics were pure opportunism. This was the heritage bequeathed by its founder, a plotter by the name of Hassan al-Banna, a chameleon who struck deals with the monarchy even as he agitated against it. His program, he said, rested on the Quran and the gun.

Banna was struck down by assassins in 1949, at age 43. Yet his followers remained true to his vision and method. When the army overthrew the monarchy in 1952, the Brotherhood thought its time had come. But the military despotism of Gamal Abdel Nasser had other plans. The Brotherhood was proscribed, and many of its adherents were sent to the gallows, while thousands were dispatched to prison camps.

This lashing by Nasser would mark the Brotherhood. In the upheaval against Hosni Mubarak, the Brotherhood equivocated. It kept its distance from Tahrir Square and courted the army. It made a pledge that it would not compete in the presidential election, only to break that pledge. It gave assurances that it would not field a full slate of parliamentary candidates, and that assurance, too, was cast to the wind. Luck delivered the Brotherhood the presidency—the self-inflicted wound of the liberals who ran three candidates in the first round and divided their own ranks.

It was then that the judiciary struck. It dissolved the parliament which had given the Brotherhood and the Salafis a decisive majority. The judiciary was two things at once: the bastion of a secular bureaucracy together with holdovers from the Mubarak dictatorship. The Brotherhood had prevailed but carried with it the reflexes of paranoia and the suspicion that the secular elites were determined to rob it of its victories.

Mr. Morsi's late-November "constitutional declaration," which put his decisions above judicial review, was born of a suspicion that the judiciary was on the verge of dissolving the assembly tasked with drafting a new constitution. This pre-emption was not wholly in error. Women and Copts and secularists had walked away from the assembly, leaving the Brotherhood and its allies to draft a constitution cut to their own vision. Mr. Morsi, recognizing the opportunity, offered the Egyptian people a compromise: He would rescind the provisions that gave him extrajudicial powers while sticking to the referendum on the constitution.

Egyptians don't really know the balance of forces in their own homeland. Theirs is a polarized country, with reformers and would-be democrats vying for power with Islamists and a still-powerful military. Is Egypt embodied in Mohamed ElBaradei, the former head of the International Atomic Energy Agency who returned home after a long sojourn abroad, or in Mr. Morsi?

Those young women who braved custom and prohibitions and sexual harassment to make a stand, time and again in Tahrir Square, are faithful daughters of Egypt. Yet so are the women of the Muslim Brotherhood. Is Egypt to be ruled by Islam's Shariah law or by the Napoleonic Code that has dominated its judicial culture? The ballot is being asked to adjudicate fundamental schisms in a deeply divided culture.

This is no time to lament the passing of the dictatorship. These are not the failures of democracy that we are witnessing in Egypt. These are the delayed consequences of a tyranny that took from the Egyptians their sense of political efficacy, and raised them to a culture of conspiracy and scapegoating.

When the Muslim Brotherhood's bullies accuse the demonstrators against Mr. Morsi of being agents of foreign embassies, they fall back on a page from the playbook of Hosni Mubarak. For three decades, the deposed dictator fed his country this sort of political diet. That assertion of extraordinary powers by Mr. Morsi right after he had brokered a cease-fire between Israel and the warlords of Hamas was vintage Mubarak: moderation in foreign policy as an alibi for domestic repression.

Meanwhile, President Barack Obama waxes lyrical about the pragmatism of Mr. Morsi, his engineering background and the precision of his scientific mind. That, too, harks back to Mubarak. Our officials never caught on to the Egyptian dictator's double-game of aiding and abetting a culture of anti-Americanism and anti-modernism (and heavy doses of anti-Semitism) as he feigned to be our man on the banks of the Nile.

Hovering over this great standoff is the army—arbiter of political life. In August, Mr. Morsi sacked its top commanders, giving command to a new generation of officers. Blessedly, this is not the ruthless, sectarian army of Syria's Bashar Assad. It is led by an officer corps that takes to heart its image of itself as the "protective shield of the country."

In that vein, the new defense minister and commander of armed forces, Gen. Abdel-Fattah el-Sissi, has called on Mr. Morsi's followers and their secular rivals to come together for "humanitarian communication and national coherence in the love of Egypt." Love aside, the army has set the parameters: It will insist on its own privileges and autonomy while putting Mr. Morsi and his rivals on notice that there are limits to its patience.

Countries don't live in constitutions. The inherited habits and traditions shape the life of nations. The dueling crowds taking to Egyptian streets are not fighting over a mostly anodyne document (one of its 236 articles stipulates that "everyone has the right to play sports"). Theirs is a big fight over this burdened yet proud land, another chapter in Egypt's Sisyphean struggle to find a way out of the destitution and despotism that have been its fate for far too long.

Mr. Ajami is a senior fellow at Stanford's Hoover Institution and the author of "The Syrian Rebellion" (Hoover Institution Press, 2012).

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