With early election results hinting at the shape of Egypt's first parliament since the fall of Hosni Mubarak, the U.S. faces the task of navigating the dynamics between Islamist parties poised to win a commanding number of seats, skeptical liberals and a ruling military that has appeared reluctant to relinquish power.

Central to the emerging political order will be the struggle between democratically elected officials and the Supreme Council of the Armed Forces, or SCAF, the country's interim military rulers. SCAF has faced escalating criticism for impeding the transition to civilian rule and attempting to sustain its authority by carving out permanent powers. After protesters flooded the streets in the days preceding the election, the Obama administration upped the pressure on SCAF with a statement urging a swift transfer to civilian rule in a just and inclusive manner.

The U.S. has long been a stalwart supporter of the Egyptian military, viewing the force as a bulwark of regional stability. Successive administrations have furnished it with nearly $20 billion since 1998, and the Obama administration requested an additional $1.3 billion for 2012. But some are beginning to question the wisdom of unflinchingly supporting an institution that has violently cracked down on protesters, re-instituted a hated emergency law and sought to heavily influence how a new constitution is drafted.

I think there is continued reluctance to revisit the issue of conditionality on aid, especially military aid, and that's something the administration needs to consider if the SCAF is intent on hardwiring a political role for themselves into the process that preserves their privileges and shields them from transparency and oversight, said Mara Revkin, assistant director of the Atlantic Council's Rafik Hairiri Center for the Middle East.

Many believe that the SCAF has been working to blunt the influence of Islamist parties like the Muslim Brotherhood, in part by exploiting fears among the country's secular and liberal elements of an Islamist-dominated government. Mubarak employed a similar strategy of posing a stark choice between his regime and the type of Islamist government of which U.S. policymakers were wary. But embracing Egypt's democratic aspirations will include acknowledging that Islamists -- both the more moderate Muslim Brotherhood and ultraconservative Salafi parties -- are likely to comprise a substantial part of the new government.

The Egyptian Democracy's Growing Pains

The United States certainly does not welcome a stronger role for the Islamist parties in Egypt, said Marina Ottoway, director of the Middle East program at the Carnegie Endowment for International Peace. But I think its recent statements suggest that the administration realizes that it cannot continue stonewalling the Muslim Brotherhood and opposing the role of the Muslim Brotherhood the way it did in the past.

At the same time, the U.S. will likely continue to look to the SCAF as a guarantee that things are not going to go too far, said Ottoway. She argued that the military has overplayed its hand with provocative moves, like publicly seeking to extend a longstanding policy of having its budget shielded from oversight, that inflamed public anger and forced the U.S. to react.

The issue is how openly the military is going to continue being a major political player, Ottoway said. Because if it continues to be a major political player behind the scenes while still respecting the façade of democratic government, the U.S. is not going to say too much about that and probably tacitly would approve that.

So far, the SCAF has remained a potent political force. In the run-up to the elections the Muslim Brotherhood faced criticism for striking a deal with the military to accelerate the timetable for presidential elections. The compromise angered many who believed holding elections sooner would favor the better organized Islamist parties, and the perception that the Muslim Brotherhood was being overly accommodating was sharpened by its reluctance to endorse or join widespread popular protests.

Everyone in the run-up to these elections to one extent or another was looking for support from the military, said Daniel Brumberg, a professor of government at Georgetown University and an advisor at U.S. Institute of Peace's Muslim World Initiative, adding that liberals were divided over whether to align themselves with the military.  It's easy to perceive this as a coherent strategy of divide and rule by the military, but it's really an outgrowth of the propensity of all the parties to look to the strongest party to support them.

Brumberg predicted an expanding rift between the Muslim Brotherhood and the SCAF as the Brotherhood seeks to distance itself from the military. An early clash will likely come as part of the ongoing debate over how the constitution will be drafted. In a preview of the strife, members of the Supreme Council recently released a proposal to draw most of the members of the constitutional committee from outside of parliament. The move was seen as an attempt to dilute the Muslim Brotherhood's clout, and a spokesman for the Brotherhood said the proposal violated the people's will.

Still, it's unclear to what extent the SCAF will insert itself into the political process. Brumberg said Egypt is at the beginning of a long process of slowly whittling away at the military's pervasiveness.

The military would prefer to continue to exercise indirect influence, said Brumberg. They'd like to get out of the business of governing and still exercise power, especially when institutions are emerging and the military can't predict how they will behave.

Because the military has for so long functioned as Egypt's most powerful institution, it'll continue to play an assertive role predicted Joshua Stacher, an expert on Middle Eastern Politics at Kent State University. He argued that the military and related institutions, such as the Minister of the Interior, are so deeply entrenched and unaccountable that little will change.

With the generals being the architects of this system that will preclude democracy, it is essentially maintaining the exact same national security stability parameter that has guided American foreign policy in the region, Stacher said. There are larger structural factors governing this system that no election can change.