At the same time, the court issued a ruling that will allow Ahmed Shafiq, the last prime minister to serve under former President Hosni Mubarak, to run in the upcoming presidential runoff, scheduled for June 16-17. In a news conference, Shafiq said Egypt's institutions would prevail and that the military and the security forces would be the ones to protect the electoral process. 

Egypt's military has the least amount of control when the country goes to the polls. Through parliamentary elections the MB, together with Egypt's Salafist faction, the al-Nour Party, came to dominate parliament. And MB candidate Mohammed Morsi had a strong chance of beating Shafiq at the presidential election polls.

The military's authority instead comes from its institutional leverage. The MB may have had nominal control over the parliament, but the military's influence over the judiciary effectively has nullified any parliamentary move the MB attempted. Similarly, the military is using its institutional strength to keep the drafting of the country's constitution out of the MB's control.

The SCAF could not be confident that its preferred candidate, Shafiq, would beat Morsi in the presidential runoff. The SCAF may be contemplating that the best way to protect its authority in the system is to back the MB against a wall, first by pushing ahead Shafiq as a legitimate candidate, then by threatening to dissolve the MB-controlled parliament and finally by establishing itself as the final arbiter in the constitution-drafting process.

The main question moving forward is whether the MB is ready for the grand bargain that the SCAF is trying to impose on the Islamist party. The SCAF appears willing to risk an MB presidency, so long as the MB cedes primary authority to the military in drafting the constitution, which will ultimately decide the balance of power among the military, parliament and presidency. The dissolution of parliament is a threat directed at the MB: If the MB accepts the military's demands on the constitution, then the SCAF could allow the parliament to remain as is; if not, it could dissolve parliament and schedule another round of parliamentary elections. In another round of elections, the MB would likely come out with another strong win. Only this time, the elections would theoretically take place within a constitutional framework shaped by the SCAF.

The MB likely anticipated that the SCAF would make such a move in the lead-up to the final vote on the presidency, but it does not appear to have had a prepared response. It is now up to the MB to decide whether it can accept the SCAF's ultimatum or whether it will resort to demonstrations on the streets, something of which many Egyptians have already grown tired. And this time, the MB could be making that decision without its parliamentary leverage.