A supporter of deposed Egyptian President Mohammed Morsi prays prior to the “iftar” fast-breaking meal at a sit-in protest at the Rabaa al Adweya Mosque in Cairo on July 28. (Ed Giles/Getty Images)

More than three weeks after the military coup that ousted this nation’s first democratically elected — and Islamist — president from power, the roots of a violent insurgency are burrowing fast into the sands of Egypt’s Sinai Peninsula.

The rapid thud of machine-gun fire and the explosions of rocket-propelled grenades have begun to shatter the silence of the desert days and nights here with startling regularity, as militants assault the military and police forces stationed across this volatile territory that borders Israel and the Gaza Strip.

The emerging Sinai crisis gives Egypt’s military a pretext to crack down on Islamist opponents across the country, including in Cairo, where at least 72 people were killed over the weekend when security forces opened fire on demonstrators rallying in support of ousted president Mohamed Morsi.

Egypt’s interim government issued a decree Sunday that granted the military the power to detain civilians, state media reported. Analysts and rights activists said the decree suggested that a state of emergency, a tool that the regime of now-deposed autocrat Hosni Mubarak had used for decades to silence opponents, might soon follow.

But in the Sinai, where the re­action to Morsi’s ouster turned deadly within days of the coup, such state-sponsored violence and repression is likely to only feed the conviction of militants, who see themselves as waging a war against a despotic and irreligious military regime.

In the Sinai, long Egypt’s most elusive and neglected region, a familiar cycle of repression has already taken hold.

The military has clamped down hard on all routes in and out. And Saturday, the armed forces launched Operation Desert Storm in the peninsula, ­according to the state-run al-
Ahram newspaper. The operation got underway after millions of Egyptians took to the streets Friday to heed the military’s call to give it the popular “mandate” to crack down on violence and “terrorism.”

Interior Minister Mohamed Ibrahim said Egypt’s security forces have been given permission to confront those who threaten the state’s “stability.”

“The people have given the army and the police a popular mandate to stand firmly against anyone who shakes the stability of the nation with terrorist or criminal acts,” Ibrahim said Sunday at a graduation ceremony for police recruits.

Backlash over coup

Bedouin leaders and Islamists in the Sinai say locals have been angered by the coup because it brought an end to Egypt’s nascent democracy — a concept that was slow to catch on in this deeply conservative territory that has long been suspicious of Cairo.

Many others, particularly Bedouin smugglers, in a population long accustomed to sweeping arrests, state-sanctioned discrimination and torture under Mubarak, say that they tasted freedom in the anarchy that prevailed under Morsi and that they are determined to avoid a return to the past even if it costs them their lives.

Sinai residents say “operations” under Morsi were more propaganda than action. But local leaders and rights groups fear that the military’s ongoing operation could target the Bedouin as a whole, rather than the 100 or so militants residing among them.

Since Egypt’s armed forces ousted Morsi on July 3, militants have launched dozens of attacks on military and police checkpoints and bases across North Sinai, killing dozens, according to state health officials, and underscoring the potential for widening violence across the country as Islamist anger grows.

Lawlessness, smuggling and militancy have thrived on the peninsula since the 2011 fall of Mubarak’s regime.

Bedouin arms dealers who are sympathetic to the militants said in recent days that fighters have launched shoulder-fired anti­aircraft Stinger missiles (known to the U.S. intelligence community as MANPADs) at military aircraft, laid improvised bombs along roads traversed heavily by troops, and fired barrages of bullets and RPGs at security personnel stationed here.

On Sunday, a police commander who spoke on the condition of anonymity said police had located a fourth bomb outside the Sheik Zweid village police station in less than 48 hours. The first three exploded, injuring several police officers, the official said.

Both police commanders and Bedouin leaders say the militants are a minority in the desert peninsula; the latter group says the militants consist mostly of locals who operate in small cells, with little to no command structure. But Bedouin leaders fear that the territory’s population may soon get swept up in the military’s crackdown, escalating the conflict into a wider war.

On a night last week, militants struck the Hay al-Safa military base near Rafah with an RPG and then gunfire. Hours later, they struck again — with what local arms dealers said were armor-piercing bullets. Families living in the area said they have grown afraid to transit through security checkpoints at night, lest they get caught in the crossfire or get targeted by nervous troops. At least 10 civilians have died in the violence this month.

‘Back to square one’

Unlike mainland Egypt, where Morsi supporters have staged thousands-strong protests that have shut down major roads and convulsed cities from Cairo to the Nile Delta, the Sinai has quickly taken its dissent to a more violent level.

Local Bedouins say it is the route borne of the territory’s cyclical history of state repression and a natural response from a local population flush with weapons and budding extremist groups.

“Protests aren’t really in our nature,” Abu Ashraf, a powerful tribal leader and smuggler in North Sinai, said last week using his nickname. “Our nature is . . .” he said, then stopped, smiled and pantomimed firing a gun.

In the wake of the coup, Egyptian security forces locked down the single bridge that connects the peninsula to the mainland and set up a battery of checkpoints along the highways that link Cairo to the Suez Canal, and onward across North Sinai, where soldiers check IDs and sift through luggage in the trunks of cars. They shine strobe lights into vehicles at night. The Sinai Bedouin feel as if the state is targeting them — again.

Analysts and local political leaders in North Sinai interpreted the call by Gen. Abdel Fatah al-Sissi, Egypt’s military commander, for a mandate to fight terrorism as a signal that a Mubarak-style crackdown was imminent. “I think Sissi wants public cover for his bloody work,” said Ahmed Salem, a spokesman for the Muslim Brotherhood in el-Arish, capital of North Sinai.

As much as the Sinai insurgency derives from militant anger at Morsi’s ouster, it is also a preemptive backlash rooted in fear, say Bedouin leaders who sympathize with the militants.

“People here have gotten some freedoms, and they will not allow those to be taken away now,” said Mohamed, a fundamentalist sheik in North Sinai who requested that his last name not be used. “The coup took us back to square one,” he said, and the Sinai’s Islamists are expressing anger at the military “in any way they can.”

“If the state does not reverse al-Sissi’s mistake, there will be more for them to endure,” he said.

Morsi’s rule offered some respite from the repression — a new kind of freedom, some Bedouin leaders said. He didn’t deliver the roads, schools or hospitals that local leaders say would help break the territory’s cycle of violent resistance. But he left them alone.

“Nothing happened the year that Morsi was in power,” said one Bedouin smuggler who spent eight years in prison under Mubarak. “Morsi had no control here. But at least he didn’t insult or arrest anyone. When you would pass by the checkpoints, they would respect you. Now we’re back to the way it was before.”

Steadily increasing violence

The military says its crackdown is necessary to fight terror, but the Bedouin here say it only adds fuel to their rebellion, in a cycle that may soon spiral out of control.

Security officials say they have seized Syrian, Palestinian and even Russian fighters in the Sinai since Morsi’s ouster. They have accused the Muslim Brotherhood, which backs Morsi, and the Islamist militant group Hamas, which controls the Gaza Strip, of orchestrating the violence, and say that many of the Sinai’s fighters are well-trained jihadists.

Last week, the Interior Ministry said a “car accident” in the South Sinai resort town of Sharm el-Sheikh led to the arrest of a jihadist who had fought in Syria. On Sunday, a police official said security forces had killed 10 “jihadists” and arrested 20 others over the weekend.

The police also have blamed the Brotherhood for the deadly weekend clashes in the Egyptian capital, sparked by police attacks on demonstrators.

The Brotherhood says it does not condone violence. “We do not support, and we do not accept it, even if it seems like the violence is in support of us,” said Salem, the spokesman.

But the Sinai, he said, was beyond the group’s control. “We had tried to tell them that democracy would give them another chance to be good people and to be involved in society,” he said of the region’s smugglers and fugitives. “But this coup made them lose faith.”

And the violence is steadily increasing. Last week, a car exploded on a rural road through the sand dunes that armored vehicles regularly transit to carry supplies to troops stationed at a gas pipeline that had come under repeated attack in the year before Morsi’s presidency.

Local villagers speculated that the three men in the car — all killed in the blast — were in the process of laying a roadside bomb when it exploded prematurely. State media reported that the “terrorists” were driving a car containing a bomb that detonated near a police training camp.

“The military is afraid that what’s happening here will spread to the rest of the republic — from clashes to car bombs,” Abu Ashraf said. And if Morsi isn’t returned to power, Abu Ashraf and other tribal leaders said, car bombings probably will ensue.

Others said sectarian violence also would flare in the absence of a political solution. Militants fatally shot two Christians in North Sinai this month. Egypt’s state-run Middle East News Agency said Sunday that a third had been kidnapped. “There is a sense here that the Christians played a big role in the coup,” said Mohamed, Abu Ashraf’s brother. “I expect there to be more Muslim-Christian violence in the future.”

At a police station that has come under attack almost every day in the center of el-Arish, plainclothes officers huddled in the main corridor on a recent day, fearful of the next attack. Their two armored vehicles sat abandoned outside.

“The biggest problem that we’re facing is that the people are not helping us,” a police commander said, speaking on the condition of anonymity. Sometimes the attacks are directed from neighboring rooftops, he said.

At the door, an officer paced nervously with a Kalashnikov. The commander held up a twisted piece of metal that appeared to be the tail of an RPG — one of two missiles to strike the station the day before. In a separate attack the same day, an officer was fatally shot on the roof.

When a call came in that the station might soon come under attack, the officers quickly grabbed more Kalashnikovs and strapped on old flak vests. “You have to leave here now. There are armed men on the way,” the officer told a visiting reporter. Then they locked the gate.

Sharaf al-Hourani and Lara El Gibaly in Cairo contributed to this report.