The protests are a run-up to the elections for a civilian government. An issue is that the military is setting itself up to be independent of the civilian government.
Although its powers will be limited, parliament is likely to find itself battling over the shape of a new cabinet which the army has the power to pick and over the extent the army will seek to enshrine powers for itself in a new constitution.There is more analysis as to the current social and political climate in Egypt here.
The new parliament will be responsible for picking a 100-strong constituent assembly which will write the new document.
But politicians were enraged this month when the army-backed cabinet proposed principles for a new constitution to shield the military from civilian supervision and to give it a broad national security remit that analysts said would give the army a pretext to undermine a civilian government.
The cabinet has backtracked after the uproar. The army has repeatedly said it has no interest in holding onto power. But the concessions and reassurances were not enough to deter this weekend's protests, or the violence that followed.
Some expect the debate over the army's role to last years.