Mohammed Morsi is not the closest male descendant of the last Pharaoh, nor an heir of the Mohammed Ali dynasty, nor is he from the ‘superior breed’ of military men who overthrew the last monarch. His election as president in June amounted to a dramatic shakeup of political tradition: Mohammed Morsi is Egypt’s first democratically chosen leader since the beginning of history.

Yet the unusual ceremonial protocol around his assumption of office reflects the bruising new political lineup that has taken shape since the sudden collapse of Hosni Mubarak’s thirty-year rule. At the insistence of the generals of the Supreme Council of the Armed Forces (SCAF), Morsi took the office not before the elected parliament—which had been dissolved by a court ruling—but at the Supreme Constitutional Court. Morsi, in turn, orchestrated a symbolic swearing-in before the revolutionary throngs in Tahrir Square.

Indicating the real power in the new lineup, one of Morsi’s first acts as president was to pay a call on SCAF chairman Field Marshal Mohammed Hussein Tantawi, rather than the other way around. The two men represent the main political powers in the ‘new’ Egypt: the eighty-four-year-old Muslim Brotherhood, by far the best organized political group in the country, and the military establishment, deeply entrenched in Egyptian society since the 1952 Free Officers coup against King Farouk.

Thus far, SCAF and the Brotherhood broadly cooperate. Unlike the military crackdown after Islamists sought power through the ballot box in Algeria twenty years ago, SCAF has accepted the Brotherhood’s political rise. For its part, the Brotherhood is cautious about calling for an Islamic revolution or uprooting Mubarak’s old guard. But the two forces have been on a collision course since January, when the Brotherhood’s Freedom and Justice Party and the Salafi Al-Nour Party captured 70 percent of the seats in the People’s Assembly.

SCAF and a SCAF-appointed government hindered the independence and legislative efforts of the People’s Assembly, whose ineffectiveness in turn seriously dented the Brotherhood’s popularity. Disillusion among supporters and increased worries among non-supporters about Islamist hegemony over all state institutions dealt a major electoral blow to the Brotherhood in the first round of the presidential balloting in May: compared to the 10.1 million Egyptians who voted for the Brotherhood’s list in the parliamentary election, only 5.7 million cast ballots for Morsi just four months later.

But the coup de grâce, which exposed what SCAF may have been planning all along, came when the judiciary stepped in to further compound the chaotic transition and effectively become SCAF’s proxy in the struggle against the Brotherhood. Days before the presidential election run-off between Morsi and Ahmed Shafik, a former Air Force commander, the Supreme Constitutional Court ordered the dissolution of the Islamist-controlled parliament on a legal technicality: security forces immediately surrounded the assembly to bar MPs from entering.

A soft coup seemed to be underway. Under the pretext of filling the legislative vacuum, SCAF issued an addendum to the interim constitution giving itself far-reaching executive and legislative powers including power over the state budget and the right to form an entirely new constituent assembly to draft the new constitution. SCAF’s decree also gave the military veto power over the future constitution.

In this power struggle, Morsi is not only confronting top generals who have no intention of losing their economic empire and veto power over national security and sensitive foreign policy. He also faces the considerable weight of the feloul, the remnants of the former regime. These include business tycoons, former National Democratic Party leaders, senior media powerhouses, and government officials who reach far and deep into state bureaucracy.

In addition, a review of Egypt’s emerging political lineup remains incomplete without noting that in the June run-off more than twelve million Egyptians registered their preference for the man who served as Mubarak’s last prime minister (compared to just over thirteen million for Morsi). Shafik’s supporters cannot be pigeonholed as pro-Mubarak counter-revolutionaries, and the most powerful among them, including those who backed Shafik with money and political influence, are clearly not going gently into the night.

Another element in the mix is the community of Egyptian liberals who welcomed the revolution but have recoiled at the prospect that democracy would privilege the illiberal Islamist movement. After performing abysmally at the polls, and fragmenting as a political force, some liberals filed court challenges to Morsi’s decree reinstating the Islamist-dominated People’s Assembly. (Morsi later withdrew his decree.) The contradictions in their earnest advocacy of a civil state are evident in their preference for a military dictatorship over an Islamist democracy.

Much legal and constitutional wrangling is still to come. One of the most difficult challenges facing the constituent assembly is unequivocally guaranteeing the separation of powers in Egypt’s new constitution. Yet the work of drafting and approving a new constitution will take place in the context of SCAF’s continuing heavy hand in Egyptian politics and government.

After his inauguration, Morsi appeared side by side with Tantawi at an Air Force display marking the graduation of a new class of pilots. No doubt a customary ceremonial act for any nation’s democratically elected president. But it highlights the absurdity of how—despite a popular revolution followed by a free election for parliament and another to replace a deposed dictator as the nation’s chief executive—there are effectively two presidents in the ‘new’ Egypt.

Rania Al Malky is the editor of Egypt Monocle, a multi-platform media outlet launched in 2012. She was the editor of the Daily News Egypt.