>> For the last two years, Frontline has watched what looked like a revolution.

(men chanting) From a dictatorship... to democratic elections.

>> Dr. Mohamed Morsi.

>> Dr. Mohamed Morsi.

>> Unfortunately, he was no Mandela.

>> From the overthrow of a new president... >> We were chanting again Morsi, they were chanting against Muslim brotherhood and some people were chanting for the military.

>> To the military taking control.

What happened to Egypt's revolution?

>> Was the military responding to the will of the people or making this all happen?

(men chanting) >> And what will come next?

>> With Sisi we have something much more ominous, much more dangerous.

>> GlobalPost's Charles Sennott reports forFrontline.

>> SENNOTT: We got to really go this way.

Come on.

>> On Egypt in crisis.

.

>> SENNOTT: Two and a half years ago, I came to Egypt and witnessed a revolution.

I watched as young activists marched to Tahrir or Liberation Square.

(protestors chanting) .

>> SENNOTT: I watched as they were joined by Egyptians of all ages and all classes, men and women.

(protestors chanting) .

>> SENNOTT: I was there day and night for two weeks.

One evening, a young songwriter named Ramy Essam performed what would become an anthem of the January 25 revolution.

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>> SENNOTT: It was a time of incredible hope and high expectations.

(praying) >> SENNOTT: But I had come on a specific mission.

I had come to understand the role of the long-outlawed Islamist group the Muslim Brotherhood.

Hi, I'm Charles.

Nice to meet you.

On Tahrir Square, I found Mohammad Abbas, a leader of the Muslim Brotherhood's youth wing.

Abbas had been working alongside secular activists to help organize the revolt.

He was eager to show us what he and his fellow Brothers had contributed.

.

>> SENNOTT: Abbas pointed out how the Brothers were in charge of the security checkpoints, serving hot tea, distributing blankets, printing posters and running an emergency health clinic.

They were holding the revolution's infrastructure together.

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>> SENNOTT: At the same time, they wanted to keep a low profile.

The Brotherhood was worried that Mubarak would succeed in portraying the revolution as a Muslim Brotherhood conspiracy.

We saw this sensitivity play out when this man approached our camera, holding up his pocket Koran.

I watched as Mohammad Abbas took him aside and told him to put it away.

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>> SENNOTT: Abbas then explained what was going on.

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>> SENNOTT: The more I got to know Abbas, the more I realized how different he was than older, more conservative Brothers I had encountered in the past.

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Still, there were many on the square who feared the Muslim Brotherhood was hijacking the revolution.

I spoke to a young law student who had been here from the beginning.

So you were here on the 25th, and you saw a change here.

Tell me about that.

>> I'm afraid.

>> SENNOTT: What are you afraid of?

>> The Brothers, the Islamic Brothers.

>> SENNOTT: You're afraid of the Muslim Brotherhood?

>> Yeah.

>> SENNOTT: Why?

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>> SENNOTT: At that time, it wasn't at all clear what direction the country would take or even if Mubarak would fall.

But you couldn't help but notice that the most powerful player in Egypt, the military, was watching and waiting, contemplating their next move.

For revolutionaries, the military was a kind of unholy ally.

>> The military are not our friends.

But I think what the military began to realize when millions of people protested against Mubarak's regime and demanded his ouster was that this power, this power among the people, was a real force to reckon with.

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>> SENNOTT: On the 17th day of the protests, everyone was listening to a broadcast of Mubarak refusing to go.

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>> SENNOTT: When suddenly, Mohammad Abbas stepped to center stage.

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>> SENNOTT: He directly addressed the military... .

>> SENNOTT: ...urging them to finish the job.

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>> SENNOTT: Less than 24 hours later, Mubarak was gone.

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>> SENNOTT: Around the world, the revolution was hailed as a victory for the people: a new day in the Arab Spring.

But they didn't see what happened next.

A few hundred revolutionaries had remained camped on the square, demanding that Mubarak's regime be prosecuted for human rights abuses and corruption.

They trusted the military would continue to protect them.

But in less than a month, the Supreme Council of the Armed Forces, or SCAF, the generals now running Egypt, ordered their troops to move in.

(shouting) .

>> On March 9, you know, very infamously, the SCAF cleared Tahrir Square and took female and male revolutionaries to military prison, where many of them were tortured.

>> SENNOTT: Largely out of sight from Western media, the revolution looked like it was over before it began.

>> I mean, this was a very clear and very early signal that the junta was not on our side, that they were not supporting or protecting our revolution.

>> It was discovered what we had all as revolutionaries suspected was happening, that the army and the military police had been rounding up activists-- interestingly enough, in the Egyptian museum-- and torturing them.

That they had been establishing checkpoints on Egyptian highways and rounding up, again, activists and torturing them.

>> SENNOTT: One of those rounded up was the young singer, Ramy Essam.

>> (translated): They took me into the museum with 200 other people.

I was tortured for four straight hours.

They used different methods, like hitting me with wooden sticks or iron bars.

There is no part of my body that they did not electrocute.

The people who were torturing me were not just ordinary soldiers.

They were senior officers as well.

They tried to humiliate us and taunt us with names, trying to destroy our dignity.

They would say, "Are you happy with your revolution now?"

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>> SENNOTT: Around 150 men and women arrested on March 9 were tried and convicted in military courts and sent to military prisons.

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Meanwhile, the Brotherhood had kept a low profile.

(praying) >> The Brotherhood steered away from protests against the military.

The few times when they participated in mass protests, they were always very keen and eager on avoiding criticism of the military and silencing voices that say things like, "Down with military rule" and that kind of stuff.

>> The Muslim Brothers were the cleverest, and they were the first ones to go to the army and say, "Here, we are at your service.

We can work with you."

(praying) >> I think we need to understand that the Brotherhood doesn't have any revolutionary ideology.

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>> SENNOTT: I had seen this during the January 25 revolution.

The old guard of the Brotherhood had hung back.

I found them far from Tahrir Square at this press conference.

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>> SENNOTT: While they said they supported the protests, Mohamed Morsi, then a relatively obscure figure, explained they were working with the military.

>> Since the 25th of January revolution, they decided from the beginning to side with these strong players, which was mainly the military.

(praying) >> SENNOTT: Throughout 2011, the Brotherhood kept talking to the military, kept off the streets and outmaneuvered its political rivals.

Revolutionaries, liberals and minorities were nervous about the Brotherhood's ambitions.

.

Egypt's Coptic Christians were especially fearful.

Members of Egypt's largest minority religious group, around 10% of the population, the Copts have survived here since the beginning of Christianity.

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But in recent years, Coptic Christians have seen a steady rise in attacks by ultra-conservative militant Islamists.

Christians expected the government to protect them.

>> There've been many attacks against churches, and SCAF was doing nothing, just as the Mubarak regime did nothing, to protect the Christian population.

(protestors chanting) >> And so this massive protest began outside the TV and radio building because many people felt that the TV, state-run TV, was inciting people against minorities and against revolutionaries.

(protestors chanting) >> SENNOTT: The demonstration at the Maspero press center was dispersed by the military with brute force.

.

(people screaming) .

>> I think Maspero in October 2011 was a huge turning point.

I think it was a traumatic event for the Christian minorities, for Christians in Egypt.

This was the first time that the military had used excessive lethal force in that way.

27 protesters were killed.

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>> SENNOTT: Mina Daniel, now a celebrated martyr, was among the people protesting that night.

Mina's sister Mary remembers.

>> (translated): We came under gunfire and were pursued by armored vehicles, crashing into parked cars.

Tear gas bombs were flying.

It was a horrible scene.

I could not find Mina.

I kept calling him, but his mobile was turned off.

Then someone told me that he been taken to the Coptic Hospital.

There, I found Mina in the morgue.

He looked like he was sleeping, with a smile on his face.

I saw a lot of dead bodies around Maspero.

I saw one person shot in the neck, and the bullet hole was still visible.

I saw a lot of blood.

I will never forget that day.

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>> SENNOTT: After Maspero, no one was chanting, "The army and the people, hand in hand."

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>> SENNOTT: Six weeks later, voting began for a new Egyptian parliament.

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I was back in Egypt and found Mohammed Abbas nine months after we'd first met in early 2011.

Abbas was now running for a parliamentary seat, but he was at a disadvantage.

He had criticized the Brotherhood's leadership for its failure to speak out against military repression and he had been expelled from the party.

But he remained optimistic about the process.

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>> SENNOTT: Whether Abbas would win was unclear, but other Muslim Brothers looked to win big.

.

For the Brotherhood, it's been a long fight.

The organization was started over 80 years ago, largely as a religious movement.

Its motto: "Islam is the solution."

>> The message was a moral message.

"The time has come to return to Islam."

>> SENNOTT: But for some Brothers, the ultimate goal was to build an Islamic state.

In the 1940s, they began a campaign of violence against occupying British troops.

Then a Muslim Brother attempted to assassinate Egypt's secular president.

Gamal Abdel Nasser cracked down.

>> The organization itself was declared illegal.

Its members were rounded up, its assets were confiscated, and thousands and thousands of people were sent to prison for years on end.

>> SENNOTT: In the 1970s, President Anwar Sadat also kept up pressure on the Brotherhood.

But the movement split over the use of violence.

(gunshots) Some members left to join groups like Ayman al-Zawahiri's Islamic Jihad, responsible for Sadat's 1981 assassination.

>> We try our best to establish this Islamic state and Islamic society!

>> SENNOTT: Al-Zawahiri would later join forces with Al-Qaeda, but the mainstream leadership of the Brotherhood rejected violence and committed itself to the democratic process.

In 2005, their candidates had won 20% of Egypt's parliamentary seats.

President Mubarak, perceiving a threat, again cracked down.

He closed hundreds of their schools and clinics and arrested over 1,200 members.

.

But persecution seemed to stiffen their resolve.

In 2012, with Mubarak gone, they aimed for the presidency.

>> (all): Doctor Mohamed Morsi.

>> (laughing) >> No, I never heard Morsi's name before.

You know, the Muslim Brothers after the revolution and when presidential elections were approaching, they said they will not field any presidential candidate.

>> SENNOTT: I'd heard that before.

In fact, I'd heard it from Morsi himself back at that 2011 press conference.

You're not going to have a presidential candidate?

Why not?

>> Well, we are saying that it's most important for us to prepare the society.

Freedom, democracy and justice are required now more than just thinking about who will control who.

>> SENNOTT: Soon after, the Brotherhood reversed its position.

Morsi, a U.S.-educated engineer, was originally a dark horse candidate.

>> Nobody really saw him as the man who would take the forefront.

I mean, his nickname in the presidential race was "the spare tire" because he was the replacement candidate.

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>> SENNOTT: But as Egyptians headed for the polls, a run-off had come down to just two men: a Mubarak-era general named Ahmed Shafik or Morsi.

>> I don't believe the majority of people voted for Mohamed Morsi because they wanted him as president.

I believe it was a false choice.

The majority of people who voted for him voted for him because they didn't want the other candidate, who was the military junta candidate, Ahmed Shafik.

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>> Many people were terrified of Shafik and not happy with the prospect of the former regime returning to power.

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>> SENNOTT: The vote was extremely close.

It took one week for the results to be announced.

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(cheering) >> A group that counts its core membership at less than five percent of the Egyptian population had leveraged its way to power.

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>> SENNOTT: The long outlawed, long persecuted Muslim Brotherhood had won.

>> It felt incredible.

Here we are, the first democratically elected president in the entire history of Egypt.

The first civilian to ever head Egypt in the modern era.

And it was like stepping into the warm sunshine after a long, long, cold winter.

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>> SENNOTT: On Tahrir Square, Morsi stood before his supporters, and in a signal that he was not afraid, he showed the crowd he was not wearing any body armor.

(crowd cheering) .

>> He got elected by the people.

52% of the people, of the Egyptian people.

I don't care why they were voting against his opponent.

I mean, they elected him.

Why don't people just accept it?

>> SENNOTT: Morsi promised to be a president to all Egyptians, and President Obama hailed his election as a milestone in Egypt's transition to democracy.

He had won, but he was already facing powerful opponents.

Just a few days earlier, Egypt's supreme court, packed with Mubarak-era judges, had declared January's parliamentary elections invalid and ordered the parliament shut down.

Islamist parties, led by the Muslim Brotherhood, had won nearly 70% of the seats.

>> They destroyed parliament two days before the presidential election, and they knew that if a president comes with a parliament that's been electorally voted in, these two institutions can literally start dismantling the old dictatorship bit by bit.

And they had to dysfunction one element of that.

>> The dilemma is that the Muslim Brotherhood come to power through elections.

They're supposedly at the helm of the state.

So they are in power, but they're actually not in power.

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>> SENNOTT: Egyptians often talk of something they call the deep state: an expression that refers to elements of the Mubarak regime embedded deep inside Egypt's government.

The deep state includes the supreme court, all state-run media, the police, and at the very top, the army.

>> The term "deep state" I think originally comes from Turkey: the sense that the military is not necessarily ruling directly, but what you have is kind of underneath the surface of politics, this underlying set of structures that's running things.

>> It is much deeper than what everybody thought.

It is really very deep because it's a result of 60 years of bad governments and corruption, so you need some time and you need drastic measures in order to be able to get rid of that.

.

>> SENNOTT: Revolutionaries and liberals who voted for Morsi hoped the new president and a new constitution would restrain Egypt's deep state.

>> One of the big demands of the Egyptian Revolution was to say, "We don't want any more torture.

"We don't any more abuse by the security services.

"We don't want any more civilians being tried in military courts," and so forth and so on.

>> We wanted to have something in the constitution against torture.

We wanted to have something in the constitution against police brutality.

We wanted to have something in the constitution that would limit the power of the military.

But rather than curb the power of the military, the constitution gave the military everything they wanted.

>> Basically what the constitution guaranteed for the military was safe passage so that none of them were held accountable for their violations of our rights during the junta rule, the SCAF rule, left the military budget untouched, left any kind of civilian oversight of that budget, and allowed the militar to continue to put civilians before military tribunals, which were all things that we, the revolution, wanted to fix.

>> The fatal mistake is that the Muslim Brotherhood could have turned to us, the revolution, and could have turned to Tahrir and to tell them, "We need you to write a constitution that would limit the power of the military.

We need you to curb and cleanse the very corrupt judiciary."

We would have come to his rescue.

And instead, he tried to flirt with the police and the militar against us.

>> SENNOTT: For any leader, curbing the militar would have been hard.

In Egypt, the military is more than an army: it's big business, controlling as much as 40% of the economy.

They make cars, clothing, chemicals, metals, bottled water, and even bread.

The full extent of their empire is unknown.

>> The military is one of the top landowners in the country, and you can't even really get a proper list of military-associated industries.

And the military wants to preserve its perks, its privileges, its significant private sector economic empire, and they want to escape from civilian oversight.

>> SENNOTT: Egypt's military also receives $1.3 billion in aid from the United States and enjoys close ties with the Pentagon.

Morsi left the military untouched, but in exchange, he wanted the generals to stay out of politics.

To cement the deal, Morsi picked a new army chief, General Abdel Fattah El-Sisi.

>> And it was a relationship of trust, because apparentl according to reports, El-Sisi went out of his wa to tell Morsi that he is a pious Muslim, he's a practicing Muslim, and that in fact, even his political ideas about elections and about sovereignty are very much in alignment with that of the Muslim Brotherhood.

(protestors chanting) >> SENNOTT: Revolutionaries have long felt betrayed by the arm and the Brotherhood.

Back in Cairo in 2011, I got caught up in protests.

.

Basically, what happened was just an eruption of people saying, "That's it."

There hasn't been justice for those who were killed.

And people seem really ready to say they're not going to stop until there's justice.

(protestors yelling) .

>> SENNOTT: After Morsi's election, protests like this continued.

>> Morsi took over the Mubarak tool kit of state-controlled media, the repressive penal code, and he started using that, and he started using that against his opponents.

He would always argue that it was necessary to do that because there were enemies everywhere and the deep state was against him, but when you look even at the record of what he was able to do or the areas where he had decision-making power, it was often a decision towards a more authoritarian form of rule.

>> Unfortunately, he was no Mandela.

He did not seem to get to grips with the mien of the Egyptian, with the soul of Egypt.

We felt that he was divisive.

>> SENNOTT: It was Morsi's greatest weakness.

Egypt has always portrayed itself as a diverse, secular state where government kept religion in balance.

But Morsi had a different agenda, and his pursuit of exclusionist Islamist politics would ultimately lead to his downfall.

The showdown would come over the role of Islamic or Sharia law in a new Egyptian constitution.

.

>> Women, Christians, intellectuals, all these were sidelined in the new constitution.

They would say, "You can have liberty of expression, freedom, etcetera, if it is in conformity with Sharia."

>> There was a lot of doors that were opened to potentially scary places.

The sections in the constitution that were about women's rights stressed equality, but then they felt the need to insert language, you know, that women are equal and have equal rights and equal work, you know, equal rights to work as long as it doesn't contradict their duties at home.

You know?

Like little, obnoxious things like that.

>> SENNOTT: In the fall of 2012, Islamists began to fear that the judiciary might shut down the constituent assembly: the body drafting the new constitution.

Morsi struck a preemptive blow.

>> On the 21st of November, Morsi issued a constitutional decree that gave him a lot of powers and put him above the constitution, above the law.

>> And you can't do that.

He didn't have enough of a mandate to behave like a pharaoh.

>> SENNOTT: The declaration gave Morsi the ability to take "any and all actions" that he alone deemed necessar to protect the country.

>> We had the making of a dictator.

This went way beyond anything that Mubarak had done.

.

>> SENNOTT: One quarter of the constitutional assembl resigned in protest.

The Islamists rammed through their new constitution regardless.

>> And that was the turning point.

For me personally, that is when I said, "No, no, no, no, this cannot be my president."

>> SENNOTT: In April 2013, a group of activists started a petition calling for Morsi to step aside.

They gave their movement a name: Tamarod.

>> "Tamarod" means "rebel."

What Tamarod managed to do is that they started gathering signatures for a popular impeachment of Morsi.

>> I saw these petitions.

There was just a list of grievances and, "These are the reasons why we have lost faith in you, and we demand early elections."

>> SENNOTT: Tamarod called for mass protests on the first anniversar of Morsi's inauguration: June 30, 2013.

But Morsi and his advisors didn't take it seriously.

>> They did not really believe that the 30th of June will be a decisive day.

They thought that it will come and go.

>> SENNOTT: Member of Parliament Amr Moussa set up a meeting with the highest-ranking member of the Muslim Brotherhood, Khairat El-Shater.

>> I told him that Tamarod insisted on one point: early presidential elections.

So it was not talking about any change or forcible change in the regime, but early elections.

Early elections is a very reasonable thing.

>> SENNOTT: U.S. officials didn't think so.

Anne Patterson, U.S. ambassador to Egypt, was uncomfortable with forcing a democratically-elected president from office.

>> It was very clear from her public announcements that Anne Patterson thought that Egyptians should swallow this pill and be content with a miserable regime because the alternative is much worse for us.

>> SENNOTT: But by mid-June, Tamarod claimed to have collected 22 million signatures, nearly half of all eligible voters.

Worried about what could happen on June 30, General El-Sisi went to see Morsi and urged him to consider Tamarod's demands.

>> And that meant a change in cabinet, a prime minister from the opposition, a change in the prosecutor general, and the president actually acquiesced to all those demands.

>> SENNOTT: But Morsi refused to step aside.

>> The idea that that focused demand would be the resignation of the president to us made absolutely no sense.

If the street becomes the way of removing a democratically elected president one year into his mandate, then no other presidenc will survive in the future.

(phone ringing) >> SENNOTT: With hours to go before Egyptians took to the streets, President Obama tried repeatedly to reach Morsi.

>> He called him for three or four times.

He insisted to Mr. Morsi to receive the call.

He received it, and it was about 30 minutes.

>> SENNOTT: Did President Obama try to offer anything to allow him to hold onto power and to build a more conciliatory government?

>> We refuse.

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>> SENNOTT: The White House declined comment to Frontline, but Morsi has clung to the idea that he was the target of a U.S. plot.

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>> SENNOTT: Then came the day.

The protest was larger than anyone imagined.

(crowd roaring) >> I just couldn't believe it.

I was dumbfounded by all these people coming out.

Already, there were millions filling all the squares, the midans of Egypt.

Not only in Cairo, but in Alexandria, in the provinces, everywhere.

.

>> The mood was amazingly jubilant.

It's people power.

And this is something electrifying when you feel it.

.

>> They were chanting against Morsi, they were chanting against the Muslim Brotherhood, and some people were chanting for the military.

>> SENNOTT: At the palace, the inner circle of the Muslim Brotherhood had a different interpretation of what was happening.

>> What was happening on the street was not opposition.

What was happening on the street were disgruntled citizens that feel that the government's performance was way below their expectations.

And that wasn't the blame of the president, that was primarily the undermining of the old regime.

It was his decision not to resign.

>> SENNOTT: Instead of conceding, Morsi rallied his supporters.

The Muslim Brotherhood organized several demonstrations and sit-ins of their own.

The biggest was at Cairo's famous Raba'a al-Adawiya mosque.

.

>> There are millions of supporters of Morsi, too.

Not as large as the anti-Morsi crowd, it is true, but they're in a very close proximity.

We're talking only kilometers apart in a cit that is very congested and very, very heavily populated.

The possibility of civil war was as high as it could have ever been.

>> Egypt was really on the brink of civil war.

This regime was so divisive that for the first time, we saw Egyptians pitted against each other.

>> SENNOTT: On July 1, General El-Sisi issued an ultimatum.

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>> SENNOTT: Morsi had 48 hours to meet the people's demands, or else.

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Morsi responded, daring El-Sisi to come and get him.

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>> He made no concessions, very Mubarak style.

And you know, in a sense, the writing was on the wall when the military made that first ultimatum.

>> SENNOTT: El-Sisi pressed on, reaching out to the crowds still in Tahrir Square.

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>> The army made its appearance with air shows trailing the Egyptian flag with the colors.

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Drawing hearts.

And personally, I thought this was a bit too cheap, but apparently it wasn't.

And people thought, "That is the answer."

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>> SENNOTT: On July 3rd, an elite Army unit was dispatched to the Palace.

.

>> He didn't foresee that it would come about this way.

Members of the Republican Guard, the Presidential Guard, came into the room, told the president that he is in their safeguard, that they would not allow anything to befall him, any harm to befall him, but that they cannot let him communicate with the outside world or leave the room.

>> SENNOTT: By the end of the night, Morsi was in military custody along with a dozen other high-ranking members of the Brotherhood.

General El-Sisi took over.

.

>> SENNOTT: Tahrir Square erupted.

(people cheering) (people yelling angrily) >> SENNOTT: But at the Raba'a al-Adawiya mosque, men and women wept.

.

>> This definitely was very painful.

We lost the country on July 3rd.

But there was a quick decision made, a quick realization that we don't have to tolerate this.

We will fight this.

>> SENNOTT: The Muslim Brotherhood dug in.

.

At the Raba'a al-Adawiya mosque, they set up a field hospital, a press center, and established a kind of human shield to protect their leaders inside.

The son of a senior Muslim Brotherhood official became their principal press spokesman.

He claimed the high moral ground.

>> What's at stake here is not Morsi.

What's at stake here is the fact that for the first time, Egyptians were believing in the idea of democracy.

What guarantees do they have if the military now sets a new roadmap for a new presidential election, a new parliamentary election and a new constitution, and then if it doesn't like the results, to derail it all at once?

>> I know they still think it is the first civilian president that was ousted undemocratically, unconstitutionally and so on.

But they have to face it.

Never in human history has there been such an outpour of rage against a regime, and it happened that President Morsi was head of that regime.

(gunshots) >> SENNOTT: The first shots were fired at dawn on July 8th, just five days after Morsi's arrest and a few blocks from the Raba'a Mosque.

(gunshots and sirens) .

>> SENNOTT: The army says they were provoked.

The Brotherhood says the military started it.

Nothing was clear.

But after several hours, three soldiers and more than 50 pro-Morsi demonstrators were dead.

.

I arrived back in Egypt a few days later.

I had never seen Cairo like this.

.

Pro-Morsi marches blocked traffic everywhere.

Divisions were evident at every street corner.

.

>> SENNOTT: I wanted to know what Mohammad Abbas thought of all this.

Abbas had lost his bid for parliament and grown disillusioned with Morsi, but I couldn't imagine he was happ with a military takeover.

Mohammed!

>> How are you?

>> SENNOTT: I'm good, how are you?

I asked him about military rule.

>> (translated): We spent a year and a half under the control of the military.

We protested against them on the streets.

Now they have come back to power through a coup against an elected authority which we also wanted to see ousted, but through civil action.

This should have happened through early presidential elections.

>> SENNOTT: So you describe this as a military coup?

>> Yes, of course.

It is a military coup, nothing else.

(translated): We do not want to have a puppet president with the military pulling the strings.

This time, we won't accept a return to how it was before Mubarak's time.

(gunshots and screaming) >> SENNOTT: Later that night, Abbas and I were caught up in a pro-Morsi protest headed towards Tahrir square.

The march was blocked by police.

.

Rock throwing, tear gas and shots followed.

(gunshots) .

>> Tear gas, tear gas!

.

>> SENNOTT: By the end of the evening, another seven protesters were dead.

These confrontations were quickly becoming almost daily affairs.

>> Both sides appear to be allowing this violence to go on, and this in a way allows the military to say the Brotherhood are criminals and they all need to be locked up.

At the same time, I don't understand wh Brotherhood leaders are ordering marches and putting the lives of their own supporters at risk.

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>> SENNOTT: The next day at the Raba'a al-Adawiya mosque, the Muslim Brotherhood held a press conference.

They had wheeled out the wounded and praised their martyrs to a roomful of reporters.

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>> SENNOTT: I asked Muslim Brotherhood leader Mohamed Beltagy about the criticism that they were intentionally putting their supporters at risk.

There are people who say that this is a strateg by the Muslim Brotherhood to create martyrs for the movement.

>> (translated): It is strange that you are saying that a peaceful protester benefits from being killed, but you do not address who is doing the killing.

Who else in the world can attack peaceful protesters?

Do you want me to go home and surrender and tell myself that our reality is a military coup?

I have a right to protest peacefully and reject this military coup.

.

>> SENNOTT: I asked another of the leaders, Essam El-Erian, how long the Muslim Brotherhood could hold out.

.

(protestors chanting) >> SENNOTT: The situation was only escalating.

On July 24th, General El-Sisi called for an end to the demonstrations at the mosque and for the people to show him their support.

.

>> SENNOTT: That Friday, millions of Egyptians gathered again, answering El-Sisi's call.

>> The animosity against the Brotherhood was so intense that there really did seem to be a desire to just wipe them off the political playing field.

And I've had conversations with people where their solution is, you know, in Arabic translates to, "Just round them all up."

How do we function as a country when we've rounded up 15% of the dissidents?

.

>> SENNOTT: There was now no stopping the momentum.

A series of meetings with high-level envoys from the United States and Europe failed to convince General El-Sisi to hold off.

Threats of withholding U.S. military aid were ignored.

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Then, at 7:00 a.m. on August 14, the police surrounded the Raba'a al-Adawiya mosque.

Soldiers blocked all the exits from the square.

>> The Brotherhood felt that if we are going to die today, then there is no better place to die and there's no better cause to die for than to say, "Not all Egyptians supported this."

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(gunshots) >> SENNOTT: For over 12 hours, the protesters were subjected to tear gas and snipers.

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(gunshots and screaming) .

>> (crying): Mama!

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>> SENNOTT: The ferocity of the campaign was historic in its brutality.

By day's end, hundreds lay dead.

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The Raba'a al-Adawiya mosque was in ruins.

The Muslim Brotherhood had once again been crushed, driven underground.

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Leaders I met and interviewed are on the run or, like Mohamed Morsi, in detention, accused of treason and inciting violence.

Mohamed Abbas has fled the country.

The future, he fears, is more dictatorship.

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The deep state is still in charge.

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>> Go to PBS.org/Frontline for a closer look at Egypt's deep state.

>> It is really very deep.

>> This underlying set of structures that's running things.

>> A timeline of the two years of turmoil following Egypt's revolution.

Additional reporting from our partners at GlobalPost.

Plus watch the film again online and followFrontline on Facebook and Twitter or tell us what you think at pbs.org/frontline.

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>> For more on this and otherFrontline programs, visit our website at pbs.org/frontline.

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Frontline's "Egypt in Crisis" is available on DVD.

To order, visit shoppbs.org or call 1-800-PLAY-PBS.

Frontline is also available for download on iTunes.