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“The military did not do anything wrong,” said Eman El Mahdy, a Tamarod spokeswoman. “We tried every peaceful way to reconcile with them, to listen to them and their requests. The Muslim Brotherhood was a security threat to Egypt.”

The Muslim Brotherhood accused the army of reinstalling “dictatorial military rule.”

“We denounce all forms of violence, all acts of terrorism or sectarian strife,” the Brotherhood said in a statement.

Brotherhood supporters expressed outrage over the military’s heavy-handed crackdown.

“It was a killing of Egyptians by the military coup,” Ahmad Lotfy, a science professor at Al Azhar University, said about Saturday’s events at the al-Fatah mosque. “Sissi is a killer. He wants to be the president of Egypt.”

The United States and Europe have expressed alarm over the violence with the European Union reconsidering its aid to Egypt, officials said Sunday. Last week, Nobel laureate Mohamed ElBaradei resigned as the interim government’s vice president in response to the crackdown.

The issue now is how to move the country forward after 21/2 years of upheaval since the Arab Spring revolution ousted autocratic President Hosni Mubarak, analysts said.

The interim government rejects the idea of integrating the Muslim Brotherhood into the political process, while the Brotherhood has refused to open talks until Mr. Morsi is restored to the presidency.

Some say the crackdown on the Islamists is to ensure that they will be unable to participate in elections. The interim government’s prime minister, Hazem el-Beblawi, said Sunday that the transition administration is considering banning the Brotherhood.

“The state has taken all measures to maintain security and public order,” Foreign Minister Nabil Fahmy told reporters Sunday. “Once security is established, the political process will be reinvigorated — open to all Egyptians within perimeters of law.”

A Gallup poll shortly before Mr. Morsi’s ouster estimated his support at 29 percent, and analysts said the Brotherhood has the support of only about 25 percent of Egyptians nationwide.

“They are not as strong or as big as they seem,” said Ashraf Naguib, CEO of Global Trade Matters, a Cairo-based think tank.

The Muslim Brotherhood was the biggest player and the best-organized group after Mubarak stepped down.

“How can we ever accept them as a political party, when their own principles are not based on democratic principles?” Mr. Naguib said.

Some Egyptians say the military’s tough stance is necessary in the nation’s quest for democracy.

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