The final round of Egypt’s presidential elections, held June 16–17, was supposed to mark the culmination of Egypt's democratic transition, which began when the military pushed Hosni Mubarak aside on February 11, 2011. Instead, the showdown between Mohamed Morsi and Ahmed Shafik was not even the most exciting event in Egypt over the past week.

On June 14 the Supreme Constitutional Court ruled that the election law for individual seats in the Peoples’ Assembly was unconstitutional, dissolving the lower house of parliament. The Supreme Council of Armed Forces (SCAF) determined that this ruling applied to both houses—a case is pending against the Shura Council election law—thus erasing the most democratically legitimate parliament in Egypt’s history. By decree, the SCAF reassumed the legislative powers it handed back to the new parliament last winter.

Then late Sunday night, just as votes were being counted, the military leaders released amendments to last year’s constitutional declaration. SCAF representatives said they waited to release the constitutional addendum so as not to affect voting, but timing also coincided with early projections indicating the Muslim Brotherhood’s Morsi was in the lead.

The presidential runoff was billed as a showdown between the old regime and the Muslim Brotherhood. Shafik had been Mubarak’s last prime minister, and it was assumed that he was backed by the military. Certainly the entrenched state bureaucracy supported Shafik: the head of the Egyptian judges association even backed Shafik publicly. There did not appear to be any significant vote rigging, though the Muslim Brotherhood seemed so concerned the election would be stolen that they had observers in every polling station reporting figures instantaneously. By dawn, following the closing of polls, Morsi claimed victory.

The past few days in Egypt have shown that anything can happen—and it is still possible that Shafik could be announced the winner. The Brotherhood’s own projections claim Morsi received less than nine hundred thousand votes more than his rival, out of more than twenty-five million, and on Wednesday the Presidential Election Commission announced it will delay releasing final results until reviewing over four hundred complaints. However, it appears the SCAF recognized fixing the election was not worth the effort. Instead Egypt’s military rulers just fixed the game, as George Washington University professor Marc Lynch so brilliantly put it.

The amendments strip the president of most national-security and defense powers and freeze him out of the Supreme Council. The SCAF provided itself with control over the military budget, consultative powers for going to war and internal security deployments, as well as a veto over every line in the as yet unwritten new constitution. The new document even retroactively “legitimizes” a justice ministry decision last week to grant the military powers of arrest.

Ironically, when it had a plurality of seats in the Peoples’ Assembly, the Muslim Brotherhood’s Freedom and Justice Party (FJP) favored a parliamentary system of government with a figurehead president. Now that figurehead will be the FJP leader, and the military is the legislative body. Will this blatant power grab push the Brotherhood to confront the military? The Brotherhood and its party are talking tough on both the dissolution of parliament and the SCAF’s constitutional declaration: members of parliament may continue to hold sessions and call for mass street demonstrations against the SCAF.

On the surface, a confrontation between SCAF and the Muslim Brotherhood has been simmering for a year. Any number of events appeared to finally push that conflict to a boil; but each time one side backed down—usually, but not always, the Brotherhood.

The military has shown that it responds to mass, cross-sector movements, such as when it withdrew its first attempt to put its stamp on a new constitution. As Al Jazeera’s Evan Hill noted, the new constitutional amendments tack closely with the military’s constitutional prerogatives of the so-called “Selmi document.”

However, the SCAF backs down rarely because it is uncommon for Egypt’s disparate civilian sectors to cooperate for long. Time and again the Brotherhood, with its superior mobilization ability, joined liberals and Leftists in street protests only to sell them out for a separate deal. If Morsi becomes president of Egypt, it is likely that the Brotherhood will back down again and accept what SCAF offers: the ability to form a government and to set the domestic budget and agenda—the main focus of the Brotherhood’s “renaissance project.”

Egypt’s transition from authoritarianism to democracy should have culminated this week. Instead, it stalled. In February 2011 the SCAF “expressed its hope to hand over power within six months…” The military delayed its return to the barracks: first to give political parties time to organize before parliamentary elections, and then so a constitution could be written to outline the powers of a new president.

More than ten months past the original deadline, Egypt still has neither a parliament nor a new constitution. Last November Egypt’s military rulers promised to hand over power to a new president before July 1. In the coming weeks there will be a transfer of governing but by no means a transfer of power.

Zack Gold is a Washington-based Middle East analyst. Follow him on Twitter: @ZLGold