Confidence in the militarys leadership began to erode in the fall and hit a low in October 2011 in response to the militarys heavy-handed approach to a peaceful protest by Coptic Chrisians, who were demonstrating against religious intolerance and the burning of a church. About 25 Copts were killed and 300 injured in Cairo when security forces fired on the crowd with live ammunition and ran over protests. Days later, the military council said it would maintain control over the government after parliamentary elections and cede power only after a new constitution was adopted and presidential elections. This process was expected to extend into 2013. The moves sparked fear that the military, which still includes members of the Mubarak regime, was postponing the transition to civilian rule in an attempt to retain control and diminish the influence of the democracy movement.

In November, protesters—representing both Islamists and the liberal opposition—returned to Tahrir Square to demand the ruling military council step aside in favor of a civilian-led government. The opposition had little confidence the military would hand over power and suggested that it was actually stifling the revolutionary fervor. The demonstrations turned violent with police firing on crowds with tear gas and rubber bullets. On Nov. 21, as the protests grew in size and intensity and police were widely criticized for their crackdown, Prime Minister Essam Sharaf and his cabinet resigned. In an agreement reached with the Muslim Brotherhood, which had stepped back from the protest movement, the military council vowed to install a civilian prime minister and to accelerate the transition to a civilian government, with presidential elections being held by June 2012. Former prime minister Kamal al-Ganzouri was named to replace Sharaf, and in response to the demands of protesters, the military council transferred most powers of the president to him. The secular opposition condemned the Muslim Brotherhood for cooperating with the military, saying the