JUDY WOODRUFF: As we reported yesterday, the Egyptian government has extended its state of emergency in the country for another two months. The move comes amid an ongoing crackdown on the Muslim Brotherhood, and stepped-up jihadi attacks in Egypt's Sinai region.
In her latest report from Cairo, chief foreign affairs correspondent Margaret Warner reports on the future of the Brotherhood and political Islam in the new Egypt.
MARGARET WARNER: Patients flown in to Cairo's El Farouq Hospital yesterday seeking low-cost care and subsidized medicines. It's one of the two dozen hospitals in Egypt built and long supported by the Muslim Brotherhood.
When we visited this one two years ago, patients spoke proudly of its Brotherhood ties and high standards. But now hospital director Dr. Magbi Abdul Aziz is keeping his distance from the group.
Who operates this hospital?
MAN: We are a branch of the Islamic Medical Association. We don't receive any help from Muslim Brotherhood.
MARGARET WARNER: Signs of the hospital's Brotherhood benefactor are nowhere to be seen here, and that's true of the many vital services the group once ran or funded. Indeed, it's a dangerous time in Egypt to be associated with the Brotherhood, must less be a member.
Much of the group's top leadership is under arrest. A few remain free, but are very much on the run.
We're talking via Skype. Why is that?
GEHAD EL HADDAD, Muslim Brotherhood: It's a wanted man for saying my opinion and for standing politically in opposition to the coup.
MARGARET WARNER: Gehad El Haddad is the group's so much. The -- quote -- "coup" was the military's July 3 removal of the president, the Brotherhood's Mohammed Morsi.
The army said it was responding to tens of millions of Egyptians who filled the streets June 30, demanding Morsi resign. Then, on August 14, police forcibly cleared two large pro-Morsi sit-ins at Rab'a and Nahda in Cairo, killing hundreds and wounding many more. Since then, the security service's crackdown has intensified, forcing El Haddad into hiding.
GEHAD EL HADDAD: I haven't seen my family in over a month or my kids. I can't communicate with them because they're as well being followed. It's a police state, with everything that comes with it.
Police states never really went away in Egypt.
Heba Morayef is Egypt's country director for Human Rights Watch. She sees the logic behind the sit-in clearing, the arrest of Brotherhood leaders, the detention of an estimated 2,000 more members without charges, and suggestions about banning the group.
HEBA MORAYEF, Human Rights Watch: All of that means that somebody in the Egyptian government, within the security agencies in particular or the military, has decided that they want to exclude the Muslim Brotherhood from political space.
MARGARET WARNER: The Brotherhood should be cut out of politics for now, says Wael Nawara, politician and writer, part of the 2011 revolution that toppled longtime ruler Hosni Mubarak.
WAEL NAWARA, leading secular voice: The first chant of this revolution was about freedom. It was definitely not about some fanatic religious cult coming and telling you what you can write, which sports you can play, what your children will study at school. Morsi was trying to change Egypt from being Egyptian to being Islamist. Islam is a part of the Egyptian composition, but it's one part.
MARGARET WARNER: Even the Brotherhood's one-time ally, the fundamentalist Nour Party, supported Morsi's removal. Its media strategist, Nader Bakkar, says the Brotherhood cut itself off from too many Egyptians.
NADER BAKKAR, Al Nour party: We are not a family. We are part of this Egyptian people, even if we have our own ideas.
MARGARET WARNER: And you think the Muslim Brotherhood is a family in the sense of feeling exclusive?
NADER BAKKAR: Oh, yes. They excluded themselves from the Egyptian people, and this is one of the fatal mistakes.
AMR DARRAG, Freedom and Justice party: Still, he is actually the first and the only democratically elected president.
MARGARET WARNER: We posed that criticism, that the Brotherhood tried to ram through an Islamist agenda, to Amr Darrag, a leader of the Brotherhood's political arm, the Freedom and Justice party. He admitted it made mistakes, but sidestepped the deeper question.
AMR DARRAG: In any democratic country, do you utilize the military to overthrow the government or use the democratic means to do that?
MARGARET WARNER: He said the party would try to keep up pressure to restore Morsi with street protests.
One month after giant pro-Morsi sit-ins came to a bloody end, this is what the Muslim Brotherhood has come to, modest demonstrations at scattered times and locations around this country convened at the very last moment through social media to evade security forces. At this one on a highway in Nasr City, we found Somaia Shaker. Her husband was killed at the sit-in at Rab'a.
SOMAIA SHAKER, protester (through interpreter): They took him by motorcycle to a hospital. Somebody called me and said he was in this specific hospital and he is dead.
MARGARET WARNER: Was he shot?
SOMAIA SHAKER (through interpreter): Yes. The hospital wanted to put it in the report as a suicide.
MARGARET WARNER: Fellow protester and Brotherhood member Hesham Mahmoud Said said he fears for his safety.
HESHAM MAHMOUD SAID, Muslim Brotherhood: Can you imagine you killed -- your government killed 3,000 people in one day, one day? Some of them were my relatives, my students, my brothers, my friend.
MARGARET WARNER: There is no official count, and Deputy Prime Minister Ziad Bahaa el-Din couldn't give us one. But there was violence from both sides, he said.
ZIAD BAHAA EL-DIN, Egyptian Deputy Prime Minister: There was the police action to disperse the sit-ins, which, obviously and sadly, took more death toll than anybody would like. There was, on the same day, widespread attacks on police stations across Egypt and on churches in the south of Egypt.
MARGARET WARNER: And what about the number of Muslim Brotherhood members, Morsi supporters who are in detention without charges?
ZIAD BAHAA EL-DIN: We are under a state of emergency, and that, by definition, gives the police more powers than under normal circumstances. It is an exceptional situation. It is not one that I like.
MARGARET WARNER: Human Rights Watch's Heba Morayef, who has investigated these incidents, says some Brotherhood members did commit and incite violence, but not in the numbers to justify the widespread crackdown.
HEBA MORAYEF: There are Brotherhood members who should be held accountable, but what the government is doing is to use the individual incidents of violence to then collectively hold every Brotherhood member responsible. And it makes the prospect of political stability in Egypt so much lower.
MARGARET WARNER: For now, Gehad El Haddad says the military has pushed the 85-year-old group back into its comfort zone in opposition.
GEHAD EL HADDAD: They're trying to wipe the existent, decapitate the Muslim Brotherhood. And they can't do that. It's an idea. You can't kill an idea.
MARGARET WARNER: Do you think some will turn to violence, that we will see a rebirth of some sort of insurgency such as took place here say in the '90s?
GEHAD EL HADDAD: Nonviolence is central to the culture of the Muslim Brotherhood, so I don't think any time sooner or later, the Brotherhood is going to turn to a violent means of change. I can't say the same by other groups in Egypt.
MARGARET WARNER: But the other big Islamist force, the Nour Party, is making a bid to stay a player, participating in the military-designed road map to fashion a new constitution and elections.
The aims, says Nader Bakkar, is to keep Islamist ideas front and center in whatever comes next.
NADER BAKKAR: We wanted at that time to guarantee a certain chance for the whole Islamic stream. If we even refused to join the road map, it would take place, and the whole Islamic stream would be illusory. So we decided to minimized losses.
MARGARET WARNER: That's a sellout, says the Brotherhood's Amr Darrag.
AMR DARRAG: Even if they invited us, this is a body that is stemming out of a political -- of a coup, of a military coup. So, that's why I say that it is absolutely important for us and for all the protesters that are out on the streets right now to stick to the democratic path.
MARGARET WARNER: So, if the train is leaving the station, you just won't be on board?
AMR DARRAG: We are on board, but maybe on another train, you know? But we are going our own path.
MARGARET WARNER: A path that for the country's most enduring Islamist organization leads to an uncertain future.