Last Thursday’s decision by the Supreme Constitutional Court in Cairo that Egypt’s parliament was elected unconstitutionally and should be disbanded is a direct challenge to the Islamists who dominate the legislature. The scene is set for a new political crisis in the Arab world’s most populous nation. It is obvious that the Supreme Council of the Armed Forces (SCAF) will not allow the fundamentalist Muslim Brotherhood to take undisputed control of Egypt’s key political institutions.

The Court has also ruled that the law passed by parliament last April to ban former senior officials from holding public office was unconstitutional. This means that ousted president Hosni Mubarak’s last prime minister, Ahmed Shafiq, will be allowed to compete in the run-off presidential election Saturday and Sunday against the Muslim Brotherhood candidate, Mohamed Morsi.  Drafters of the law argued that parliament had the duty to prevent members of the old regime from returning to power, but opponents saw it as an act of political revenge specifically targeting Shafiq. “This historic ruling sends the message that the era of score-settling,” Shafiq said at his rally.

The Brotherhood called the moves a coup and vowed to rally the street against the ruling military and against Shafiq, who is widely regarded as a favorite of the generals. Yet again there are crowds of protesters in Cairo’s Tahrir Square, the scene of the revolt that brought down Mubarak last year.

Many commentators critical of the Court’s ruling have failed to note that the legal basis for the decision is fairly clear. The electoral law had set aside a third of seats for independent candidates not affiliated with any political party. In reality, however, most of those nominal independents subsequently have revealed their true colors as supporters of the Brotherhood’s Freedom and Justice Party or the Salafi Nur Party. Those parties’ systematic attempt to subvert the intent of the law by fielding their loyalists as quasi-independents is undisputable. The contentious aspect of the Supreme Constitutional Court’s ruling is its order that parliament be dissolved and new elections held for all five hundred seats, and not just for the disputed third.

The secularist officers who control the SCAF are hoping that in a new election the fundamentalists will do less well than last fall. At the moment the Brotherhood controls one-half of all seats and the hard-line Salafis a quarter. They may have overplayed their hand by promptly demanding the introduction of Sharia law, banning alcohol and swimsuits, and effectively trying to turn Egypt into a single-party state. This has scared many Egyptians who were initially supportive of last year’s protests. The Brotherhood’s popularity has also declined because it tried to dominate a parliamentary panel which had the task of writing a new constitution. The panel was also dissolved by court order, and a new one had yet to be appointed. The dissolution of parliament now raises the possibility that the SCAF will appoint its members and thus keep the drafting of the constitution under firm control.

This week’s events indicate that the legacy of nationalist secularism remains strong among Egypt’s elites. The military is both powerful and popular. If Shafiq wins the Presidency, an Islamist takeover of the state will be postponed. If there are large-scale street protests or if Morsi wins, it is an even bet that the generals will hold on to power beyond the July 1 deadline which they had set for handing the authority over to a civilian president.