CAIRO—A month of deadly conflict between security forces and the mostly Islamist supporters of Egypt's ousted president has battered the country's once-powerful Muslim Brotherhood, leaving it with diminishing prospects for restoring its former pre-eminence.

At least 42 people were killed in clashes around Egypt on Friday, according to officials, in violence set off two days previously when police raids on Muslim Brotherhood protests in Cairo left hundreds dead, in modern Egypt's worst violence in memory. As Brotherhood supporters defied martial law and faced off Friday with government security forces and civilians, leaders of the group upped the ante by announcing they were calling for a Week of Departure—protests aimed at ousting the head of Egypt's armed forces, Gen. Abdel Fattah Al Sisi.

But the group, which was the country's most popular political force as recently as two years ago, now faces an openly hostile national media, shriveling public good will and a huge security apparatus intent on destroying it. Many of its leaders are in jail. Those who remain free have been driven underground—declining to appear in public even for Friday's funeral of a top leader's daughter.

Some of these leaders met in secret Friday, said one Brotherhood leader, to debate their "alternatives and next steps."

Their moves appear limited. The group has called for its supporters to keep pressing for the reinstatement of Mohammed Morsi, the elected Muslim Brotherhood president who was removed by the military on July 3, spurring several deadly clashes in recent weeks with security forces.

By remaining on the streets, the group runs the risk of even more violence—a scenario that would not only antagonize the same polity that blessed them in elections, but also play into the government's position, increasingly voiced by Egyptians, that its security forces are battling a terrorist menace intent on seizing the state and imposing Islamic law.

But ending the protests, group leaders say, would erode the organization's claim to legitimacy. Since the Brotherhood renounced violence in the 1970s, it has sought to distinguish itself as a moderate Islamist organization deserving of a place in Egypt's nascent democracy. Without a viable political outlet, Egypt risks seeing some of the Brotherhood's vast membership radicalize and split off, said experts on political Islam.

"If the Brotherhood continues like this, it's self-suicide," said Khalil Al Anani, an expert on Islamist organizations and a senior fellow at the Washington-based Middle East Institute.

Leaders of the group have used word-of-mouth and social-networking sites to urge demonstrators not to bring weapons to protests or attack the police. While the group has said its unarmed protesters have come under attack, public anger has been inflamed by accounts of protesters using machine guns and other weapons against security forces. Egyptian state television on Friday showed images of what appeared to be pro-Morsi protesters firing an AK-47 from a bridge in central Cairo.

These protesters don't answer to the group, Brotherhood leaders have said.

"There are some young people, ordinary people, who are trying to say that it doesn't make sense to face this peacefully," said Amr Darrag, a leader in the Brotherhood's political party and a former minister under Mr. Morsi. "We are trying to calm people down and the only way is to remain peaceful. We say that we can never match the force that the security police and military have."

While Mr. Morsi's top lieutenants often boast that the majority of pro-Morsi protesters are unaffiliated "pro-democracy" activists, the presence of political independents has made the heaving crowds almost impossible to control, particularly during violent clashes with Egypt's police and military, say protesters and Brotherhood leaders.

"Yes we have guns, what is wrong with that?" Wagdy Helmy, a 26-year-old protester was camped out in a pro-Morsi tent city for weeks last month, said on Friday. He characterized himself as among the majority of protesters—"enthusiastic youth" who he said were politically unaffiliated. For these people, he said, the armed fight amounted to self-defense. "You are peaceful and then they shoot at you, so how do you get back at them?"

Brotherhood leaders remained largely out of sight Friday. The weren't seen at the funeral for Asmaa el-Beltagy, the daughter of senior Brotherhood official Mohammed el-Beltagy. She was killed in Wednesday's raid on Raba'a Al Adiwiya Square, said her grandmother, who attended the funeral.

The senior Brotherhood official who spoke of Friday's secret meeting said group leaders hadn't determined whether it was safe enough to show up at Friday's main protest site, at central Cairo's Ramses Square.

"We know there are snipers and they would like to kill the leaders," this person said.

One proposal on the table at Friday's meeting, the Brotherhood official and some protesters said, is to expand the protests by calling for nationwide civil disobedience and general strike. Such a walkout would put added pressure on the state to respond to the pro-Morsi protesters demands—but also hold the potential to further alienate Egyptians.

The Brotherhood's fall from public grace has been steep. The organization's members and their Islamist allies took the lion's share of votes during Egypt's 2 1/2-year-long transition. But late last year, when Mr. Morsi sought authority over Egypt's judiciary—which Islamists had accused of working in the thrall of Egypt's former autocratic regime—Egyptians took to the streets against what many saw as a dictatorial move.

Those protests extended into months of riots and sit-ins, pitting Mr. Morsi's Islamist political machine against the president's unelected secular opponents. Mr. Morsi end came in early July when a military coup backed by millions of anti-Brotherhood protesters pushed him from power.

The Brotherhood's defiance in the face of what it calls a military coup appears to have depleted its already dwindled reserves of public good will. Egyptians were infuriated by the Brotherhood's standing six-week protest encampment in downtown Cairo and Egypt's increasingly vitriolic media painted the two pro-Morsi sit-ins as incubators for terrorism.

Egyptian media accused the protesters of harboring weapons, terrorizing neighborhoods and committing murder and child abuse to further a sinister Islamist agenda, all of which the Brotherhood strenuously denied.

When security forces stormed pro-Morsi sit-ins on Wednesday, killing hundreds, the media and Egypt's public seemed to spare little sympathy. Secularist politicians and government officials pointed to the massive firefight as further proof of the Brotherhood's violent tendencies.

The majority of newspapers on Thursday and Friday carried no pictures of the hundreds of dead protesters, instead showing images of state buildings and churches they said were attacked by pro-Morsi protesters.

That message resonates with much of a public that has long viewed the Brotherhood as not only secretive, but all-powerful when it comes to the behavior of their individual members.

"Everything in the Muslim Brotherhood is totally centralized," said Mohammed Abul Ghar, the head of the secular-leaning Social Democratic Party and a staunch opponent of Mr. Morsi. "Every small order from Aswan to Alexandria is by the head of the Muslim Brothers."

Brotherhood leaders continue to hone their public message. Late Friday, the Brotherhood-led Anti-Coup Alliance called on supporters to withdraw from the streets after nighttime prayers. The statement spoke to Brotherhood concerns that violence may be whittling away at public sympathy, and called on supporters to "preserve human lives and reassure that our peacefulness is our strength."