CAIRO, Egypt — Egypt’s Muslim Brotherhood is in crisis.
Just days after the Egyptian army, backed by popular protests, ousted Brotherhood leader and former President Mohamed Morsi from power Wednesday, the Islamist organization’s top echelons are facing an unprecedented wave of arrests. Its media channels have largely been shut down and journalists arrested by army and police forces.
In Cairo Monday morning, 51 of the president's remaining supporters were killed after the military opened fire on a group of dawn worshippers outside the headquarters of the Republican Guard, an elite unit of soldiers that guards the president.
The Brotherhood is calling the killings a “massacre,” and field hospitals in the area have struggled to cope with the influx of casualties. The army has said it was the work of an armed gang that attacked the institution. Either way, it marked the single worst day of violence since the crisis started last week.
"The sky was thick with tear gas and bullets," said Ahmed Said, an eyewitness at the scene. "So many people died, I saw two of my brothers fall."
Witness Yehia Youssef, 24, said he was at the sit-in to defend Morsi’s legitimacy as the country’s elected leader. “But then the army shot us in broad daylight,” he said.
Left staggering and angry by the wider crackdown, the Brotherhood now faces the most critical period in its 85-year history, analysts say. Its leadership must decide whether to rebuild, or retreat from politics altogether.
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The group’s entry into Egypt’s post-revolution politics — which some say was its greatest gamble yet — could prevent it from exercising the same resilience in years to come.
"This is probably the most significant moment in Brotherhood history,” said Nathan Brown, prominent Egypt scholar at George Washington University in DC.
Founded in 1928, the Brotherhood has been both courted and suppressed by various Egyptian governments. The group spent the final years under former President Hosni Mubarak as a banned but tolerated organization with independent candidates in parliament and social welfare programs in impoverished areas.
“Decisions that are being made now by the leadership have the potential to shape political Islam both in Egypt and elsewhere,” Brown said.
When popular street protests toppled the former dictator, the Brotherhood seized the opportunity to rule Egypt as its most organized and well-disciplined political power.
The group’s political arm, the Freedom and Justice Party, won a majority in the parliamentary elections in 2011-2012. Later, they decided to field a candidate for the country’s presidency, a move many observers said spoke to the group’s desire to monopolize political power.
But shortages of basic commodities, deepening sectarianism and Morsi’s insistence on polarizing rhetoric that fanned unrest intensified opposition to his rule.
When on the anniversary of his inauguration June 30, millions of Egyptians turned out to call for Morsi’s ouster, Egypt’s military issued an ultimatum to leader: resolve the crisis within 48 hours or we will intervene for the sake of the nation.
On July 3, the defense minister announced on state television that the army was suspending the constitution, and dissolving the Islamist-led parliament.
The military takeover was followed by a swift crackdown on the Brotherhood's leadership and its channels of communication, including television networks.
Within hours, the military detained Morsi and Egypt’s prosecutor-general issued more than 300 arrest warrants for Brotherhood members.
Police arrested leading figures Saad El Katatni and Rashad Bayoumi, both of whom were later released. Security forces also detained the Brotherhood’s deputy leader, Khairet El Shater, on charges of inciting violence.
“It was a real shock,” Mohamed Abd El Razek, an anchor at the Brotherhood-owned Egypt 25 channel, said of the raids on the Islamist group’s media outlets. “Police forced their way through the doors. They waved guns in our faces and shouted insults before they arrested.”
Security forces confiscated their equipment and held the staff in an unknown location, before they were later released.
According to Razek, the swift closure of Brotherhood media outlets was intended to prevent footage of anti-military demonstrations from flashing around the world in the immediate aftermath of the coup, and to cut off established channels between Islamist politicians and their supporters.
“We thought we'd have our freedom after the January 25 revolution,” he said. “But suddenly, it feels like the military-police state is back.”
The crackdown has also been welcomed by leading opposition figures, including Mohamed ElBaradei, the former diplomat who appeared with the defense minister when the military coup was announced and is rumored to be the country’s interim vice president.
“The security people are worried: there was an earthquake and we have to make sure that the tremors are predicted and controlled,” ElBaradei told The New York Times in an interview Saturday. "They are taking some precautionary measures to avoid violence; well, this is something that I guess they have to do.”
But the violence is increasing, including clashes between pro and anti-Morsi protesters near Tahrir Square Friday, and that left more than 30 dead.
Thanks to tight internal discipline and an organizational structure, which allowed it to adapt to the changing nature of Egypt's authoritarian regimes, the organization was able to survive the often brutal oppression meted out by successive administrations.
But the internal debate that will now consume the Brotherhood will be crucial in shaping their capacity for political survival, analysts say.
“In the coming years, we're looking at a real possibility of a political process in Egypt that the Brotherhood has opted out of,” said Brown, “and that would really be the first time that has happened since the organization re-emerged in the 1970s and 80s.”
"What we are likely to see coming out of this is a Brotherhood that keeps its organizational base in tact,” said Brown. “I don't think we're going to see any split in the organization."
Hazem Kandil, a lecturer in political sociology at the University of Cambridge, says the Brotherhood will now struggle to recover from the widespread loss of trust.
"It is crucial to understand that people supported the Brotherhood because they believed that they were truly representing an Islamist alternative and would be competent at running the state," Kandil said.
For their part, Brotherhood officials are warning that the implications of the Islamist crackdown extend beyond the organization's immediate survival.
"I hope people realize that this is a major setback," said Amr Darrag, a Muslim Brotherhood leader who had most recently been appointed as Egypt's Minister of Planning and International Cooperation.
“We had a revolution for these rights,” he said. “No one should be allowed to hand them over to the military."