So the Egyptian military has deposed Morsi in a coup. Many of Morsi’s supporters are predictably refusing to accept the outcome:

The escalating tensions between Mr. Morsi’s Islamist supporters and their opponents continued to spur street violence overnight. Egyptian officials said at least 18 people had died and more than 300 were injured in fighting near an Islamist rally in support of Mr. Morsi near Cairo University. State media reported that the dead included victims from both sides and that most died of gunshot wounds.

Even before the military deadline expired, there were signs of a new crackdown on Mr. Morsi’s allies in the Muslim Brotherhood. Police officials said Wednesday that they had arrested six bodyguards protecting the Brotherhood’s spiritual leader.

It is too soon to know how much violent resistance there will be to the coup, but it seems reasonable to expect that large numbers of Morsi supporters will regard any new government created as a result of the coup as illegitimate and will seek to sabotage and undermine it. That bodes ill for religious and political minority groups that will probably be scapegoated in response to Morsi’s overthrow, since they will make for easier targets and have been identified with the coup. Perversely, the coup may have done what the Muslim Brotherhood could not have done for itself, which is to return it to the role of a persecuted opposition movement.

Marc Lynch looks ahead:

What now? There remains a very real, urgent risk of major violence and further political or even state collapse, of course. But even if the worst is avoided, Egypt faces a real risk of becoming trapped in an endless loop of failed governments, military interventions, and popular uprisings. The very idea of democratic legitimacy has taken a severe beating, and the coming constitutional reforms and new elections will not pass easily.

It is Egypt’s minorities that are at greatest risk in this unstable environment, and they are the most vulnerable to the abuses of illiberal majoritarianism and military rule.