Reports from Egypt are anything but reassuring. All indications are the differences of opinion between the military and the elected government will plunge the country again into political instability, if not a new round of turmoil.

Egypt’s top court Friday rejected a decree by President Mohamed Morsi to reinstate parliament, which the judges of the Supreme Constitutional Court — mostly leftovers from the Mubarak days — had earlier dissolved, saying a third of its members were illegally elected. The court may say it was “not a part of any political conflict”, but those closely watching the developments in Egypt since the uprising that drove Hosni Mubarak from power 18 months ago know where the court’s sympathies lie. And the military lost no time to come to the court’s defense. The constitution and the law must be upheld, said the Supreme Council of the Armed Forces (SCAF), endorsing the court’s ruling.

This puts Morsi in a difficult situation. He or his party, the Muslim Brotherhood, may not like a head-on confrontation with the generals who have run Egypt since Mubarak’s downfall, but the men and women of all political hues who crowded into Tahrir Square last year and younger members of the Brotherhood want a clean break with the past.

Morsi was sworn in on June 30, but Egypt’s first elected president had to assume office accepting severe restrictions on his authority as the generals gave themselves legislative and budgetary powers and control over the process of drafting a new constitution. In effect, the generals want to wield power behind a civilian facade.

When they say that the armed forces will not allow a “certain group” to dominate the country, as Field Marshal Mohamed Hussein Tantawi, the head of the Supreme Council of the Armed Forces, said last month, they are in effect saying that the military wants to be the dominant power in Egypt as it has been for nearly 60 years. When the military says it will not abandon its role as “the protector of Egypt”, it is signaling that it has no intention of giving an elected president a free rein.

This goes against the spirit of the Tahrir Square revolution. This goes against all norms of democracy under which the military has to accept civilian supremacy in everything, including defense and foreign policies.

As things stand now, the military will continue to enjoy all such powers at least until new parliamentary elections are held and a new constitution, setting limits on its power, is drawn up.

The generals may do everything possible to avoid new elections and drawing up a constitution. Morsi can checkmate them only if he has the broad support of all Egyptians, including the minorities, and not merely of the Brotherhood and those who believe in its ideology. He has to ensure that secularists and minorities don’t rally to the side of the army just because they fear an Islamist takeover.

Already gangs of devout young men in villages and slums have taken on a more active self-appointed role in policing their communities. Morsi must rein in them. Daily rallies held in support of SCAF should alert Brotherhood and all those who believe in democracy to the dangers that lie ahead and the challenges facing them.