The arrest on October 30 of Essam el-Erian, a member of the Muslim Brotherhood’s once-powerful Guidance Council and deputy leader of the MB-controlled Freedom and Justice Party, demonstrates the extent to which the interim government of Egypt has been able to cement its control over the country since former president Mohammed Morsi was ousted almost four months ago. In hiding since the country’s security forces stormed the Rabiya al-Adawiya encampment on August 14, Erian was captured following a tip-off—a sign of the Brotherhood’s declining ability to function, once again, as a tightly-knit clandestine movement.

Officially designated as a terrorist group and enemy of the state, the MB seems unable to adjust to pressure and revert to the old order of battle which functioned well under Mubarak. Its basic cells, seven-member local groups known as usras – originally devised by the MB founder Hassan al-Banna to indoctrinate and mobilize followers – are crumbling. A top security official who has long monitored the Brotherhood told Reuters on Monday that the usra structure has been effectively destroyed: “The Brotherhood member is taught not to think on his own, just to take orders. This is how the group functions. So if there is no one to give them orders it means the group is in trouble.”

The key order-givers—up to two thousand leading Ikhwanis—are in jail. Thousands more ordinary members have been detained and questioned as evidence is collected to use against the leadership. Observers say that on current form some two hundred MB leaders are likely to end up in court, including members of the Guidance Council and many former Freedom and Justice Party deputies. The Brotherhood’s supreme guide, Mohammed Badie, and his two top associates have been on trial since August on charges of incitement to violence and terrorism. In another sign of government self-confidence, Morsi himself will go on trial on November 4, charged with inciting MB supporters to kill protesters outside the presidential palace in December 2012. If convicted he could face the death penalty. Even if the sentences eventually turn out to be less severe, any criminal convictions would prevent the Brotherhood’s key leaders from running (under whatever label) in the presidential and parliamentary elections scheduled for next year.

The ferocity of the clampdown on the MB is partly due to the influence of General Mohamed Farid el-Tohamy (66), a sworn enemy of the Brotherhood, who was retired and investigated by the Morsi government last year. He is back, and more powerful than ever. General Abdul-Fattah el-Sisi, Egypt’s de facto leader, promptly rehabilitated his friend and former mentor Tohamy and put him in charge of the powerful General Intelligence Service (GIS, otherwise known as the Mukhabarat). As soon as he took the post Tohamy supported an uncompromisingly hard line in dealing with the MB, as evidenced in the onslaught on the encampments last August. According to a report in Wednesday’s New York Times, his opposition to the inclusion of any Brotherhood elements in the political process after the July takeover swayed Sisi, who initially appeared willing to adopt a more conciliatory line which was advocated by former vice-president Mohamed el-Baradei.

The Muslim Brotherhood faces several unpleasant choices. To continue the campaign of violent resistance would be self-defeating—as evidenced by the determined response of the security forces—and unlikely to elicit significant sympathy at home or abroad. To persevere in demanding Morsi’s reinstatement is hopelessly unrealistic. To reenter the political process, the MB would have to accept the military-backed roadmap for the country’s transition—as recently reiterated by interim vice-premier Ziad Bahaa-Eldin—which would mean admitting defeat and granting legitimacy to Sisi’s fait accompli. To cease visible activities and regroup underground would imply fresh years or even decades in the wilderness, reminiscent of the Mubarak era, which is unacceptable to the group’s younger members who’d likely seek direct action and instant martyrdom elsewhere. With most MB leaders in jail and unable to communicate among themselves or with their followers at large, those choices simply cannot be made.

Contrary to the predictions of many Western pundits and journalists, Egypt’s “deep state”—seemingly on the defensive during Morsi’s year in power—has been able to control the situation and stabilize the country (as we predicted it would be three weeks after the coup). This was in part due to Sisi’s disregard for the advice from Washington, which came at the tolerable and probably only temporary price of losing U.S. military aid. Egypt’s future president will face many challenges in the years ahead, especially in kick-starting the country’s faltering economy, but dealing with them will be easier with the Muslim Brotherhood’s ongoing demise as a major political, social and moral force.