Reuel Marc Gerecht is a senior fellow at the Foundation for Defense of Democracies. He served in the CIA’s Clandestine Service from 1985 to 1994, specializing in the Middle East.

How will the Egyptian army’s coup against the elected Muslim Brotherhood government affect Islamism, intellectually and politically the most consequential movement in the Middle East since the 1960s? Do the brethren see their fall as a rejection of their religious beliefs? Should they?

Historically, it’s impossible to imagine Islamic militancy without the Brotherhood. Founded in 1928 against British imperialism and a rapidly Westernizing Egypt, the Brotherhood became the flagship for Sunni fundamentalism. Secretive but populist, contemptuous of state-paid clergy, intellectually syncretistic (socialism, fascism and European anti-Semitism blended into their “authentic” faith), the brethren became widely popular in Egypt as the army’s experimentation with radical Arabism and crony capitalism failed.

The real strength of the Brotherhood movement, along the Nile and beyond, has always been its public faith and private virtue and its appealing historical narrative for Muslims who see the prophet Muhammad as a paragon — a people’s greatness flows from moral rectitude. The downfall of the general-turned-president Hosni Mubarak two years ago caught the brethren off guard. Thirty years ago, they opted for coexistence with the security state: Abjuring politics, they focused on missionary and social work. They became “neo-fundamentalists” who envisioned the collapse of the Egyptian police state one convert at a time. With the intense democratic debates among Arab intellectuals that followed the Sept. 11, 2001, attacks and the Iraq war, Islamic fundamentalist movements increasingly adopted a democratic lexicon and started, however tepidly, to struggle with the contradictions between popular sovereignty and the Holy Law.

The brethren’s embrace of democratic politics always hinged on an old-fashioned Sunni assumption that the majority of Muslims couldn’t be bad Muslims. The recent massive demonstrations in Egypt certainly show that many Egyptians who voted repeatedly for the Brotherhood — in parliamentary elections in 2011 and 2012, in the presidential election last summer and to adopt the new constitution in December — hit the streets against them. This has shocked some of the brethren and provoked Islamists elsewhere to reflect on the intersection of religion and politics.

Although religious tyranny secularizes society (see Christendom/the West), the Brotherhood’s “rule” was probably too short, ineffectual (real power remained with Egypt’s army and security services) and morally tepid. Women’s social status when President Mohamed Morsi fell was about the same as when he was elected. Western “bikini tourism” and easy access to alcohol — controversial issues for Islamic fundamentalists — had not been touched. Tied up in the elemental problems of governing with little authority, the Brotherhood hadn’t really formulated, let alone tested, its conception of the “good life.”

For the secular opposition, this is a big, and probably lethal, problem. In the Islamic Republic of Iran, religious zeal among the common faithful has been burned out by the Iran-Iraq war of the 1980s and three decades of corrupt, oppressive clerical rule. Onetime Islamists have become trenchant critics of theocracy. Similarly, the appeal of secularism in Iran was widespread in the 1950s and ’60s but died slowly under the shah, as a Westernizing dictatorship and the economics of a modern centralized state bulldozed traditional society and kindled a politicized religious awakening. The electoral triumph of Turkey’s Islamist-friendly Justice and Development Party was also long in coming, partly because the Turkish military checked the democratic expression of the country’s religious hinterland. It is inconceivable that the corrupt and cruel Egyptian army could stage-manage a better evolution to a non-Islamist democracy than had the Turkish army, which was, comparatively, neither corrupt nor cruel.

What the Arab Middle East has not seen since before World War I — when Egypt experienced a brief efflorescence of secular liberalism — is a real competition between Arab liberals and devout Muslims who see politics largely as an extension of their faith. The latter is, unquestionably, still a majority in Egypt. (The Holy Law is the law for most Egyptians, who have been living outside the country’s calcified, ineffectual legal system of imported European codes.)

Many young secular Egyptians — and their Western fans — appear not to know this. They imagine having a liberal democracy in which advocates of sharia and the Islamic tradition cannot win an election, write the constitution or otherwise shape society except along secular lines. Westernization has been so successful in Egypt that perhaps a third of the population may no longer share basic cultural mores with the religious majority. Egyptian liberals, and the rest of the intellectually diverse opposition to the Brotherhood, turned to the street and the army — Egypt’s real ruler since 1952 — to compete. It’s an umbilical relationship that is now unlikely to be broken.

Morsi, an incompetent, boring and inarticulate demagogue, will not return. But Egypt’s enormous systemic problems remain. The military may try to jury-rig elections in which the brethren could compete but not triumph. Mindful of recent Turkish history, senior officers will not allow vengeful Islamists to compete, win and neuter the army. Egypt’s problems are now the responsibility of the military and Egyptian liberals. The odds are that they will fail abysmally, and in their failure, the Brotherhood and other Islamists will recapture the street.

Egypt’s experiment with democracy is probably over. Egyptian secularists may win the next election, but many — probably most — Egyptians will see the vote as illegitimate. Islamism grew strong in Egypt in opposition to unlawful power. Islamists may return to violence — the holy-war arguments advanced by the Brotherhood theologian Sayyid Qutb are more readable now. More likely, the brethren will rally their followers in the streets and return to neo-fundamentalism, biding their time until the Egyptian army cracks. Contrary to what the Facebook liberals proudly boast on Tahrir Square, the game is far from over.