Ian Black writes: Egypt, a Cairo wit quipped recently, is “lost in transition”. The serious point is that although Hosni Mubarak stepped down in February 2011, the country’s progress from autocracy to democracy has been halting and complicated by tensions, divisions and violence at every turn.

Now, just two days before the runoff round of an already polarised presidential election, an extraordinary twist has created profound new uncertainties. The most dramatic interpretation is that it spells a decisive victory for the forces of counter-revolution. “It is like The Empire Strikes Back in the Star Wars saga,” commented the popular blogger Zeinobia. Others denounced it furiously as a judicial coup.

It is not surprising that the constitutional court decided that Ahmed Shafiq, Mubarak’s last prime minister, is eligible for the race, having ruled against a “political isolation” law that would have prevented him seeking office as a member of the old regime.

The judges, appointed under Mubarak, are widely seen as representative of the “deep state” that has survived the convulsions of the Egyptian chapter of the Arab spring to manoeuvre, manipulate – and retain power – behind the scenes.

Shafiq’s battle against Mohamed Morsi, the candidate of the Muslim Brotherhood’s Freedom and Justice party, has been dubbed a “nightmare scenario” by Egyptian commentators who see it as a throwback to the bad old days when the military-backed presidency was ranged against the world’s oldest Islamist movement, with little else in the way of independent political forces between them.

But the court’s second ruling is far more volatile in its implications. The dissolution of the entire parliament – not just byelections for the third of MPs deemed to have been improperly elected – means that the Islamists who dominate it, from the Brotherhood and the hardline Salafi Nur party, will feel disenfranchised and cry foul.

David Ignatius spoke to Khairat el-Shater, the leading strategist of the Muslim Brotherhood: Shater was conciliatory when he talked about a Brotherhood victory. “Egypt is too big a responsibility for one group to lead it. It has to be a coalition,” he asserted. He didn’t talk about a Muslim state; indeed, the word Islam barely surfaced in the 90-minute conversation. Yet the conversation was scary when he talked about what would happen if the Brotherhood should lose.

But turmoil is ahead for Egypt, he says, if Ahmed Shafiq, a hard-line former prime minister, appears to win Sunday’s runoff. I say “appears” because Shater was already accusing Shafiq of “soft-rigging” the polls before Thursday’s court ruling. And he made a not-so-subtle prediction that if the Brotherhood’s rival should win, there will be violence.

The Egyptian people “will not accept Shafiq as president,” he said flatly. “From the first day of the announcement, people will be back to Tahrir Square. If the choice of the people is to protest, we will join the people.” He warned that foreign countries shouldn’t make quick moves to recognize Shafiq.

“The coming revolution may be less peaceful and more violent” than the one that toppled Mubarak, Shater predicted. “It may be difficult to control the streets. . . . Some parties, not the Muslim Brotherhood, may resort to further violence and extremism. . . . When people find that the door to peaceful change is closed, it is an invitation to violence.”