The jihadis in Egypt's North Sinai had killed hundreds of soldiers and police officers, pledged allegiance to the Islamic State, briefly seized a major town and begun setting up armed checkpoints to claim territory. In late 2015, they brought down a Russian passenger jet.
Egypt appeared unable to stop them, so Israel, alarmed at the threat just over the border, took action.
For more than two years, unmarked Israeli drones, helicopters and jets have carried out a covert air campaign, conducting more than 100 airstrikes inside Egypt, frequently more than once a week -- all with the approval of President Abdel-Fattah el-Sissi.
The cooperation marks a new stage in the evolution of their fraught relationship. Once enemies in three wars, then antagonists in an uneasy peace, Egypt and Israel are now secret allies in a covert war against a common foe.
For Cairo, the Israeli intervention has helped the Egyptian military regain its footing in its nearly five-year battle against the militants. For Israel, the strikes have bolstered the security of its borders and the stability of its neighbor.
Their collaboration in the North Sinai is the most dramatic evidence yet of a quiet reconfiguration of the politics of the region. Shared enemies like the Islamic State, Iran and political Islam have quietly moved the leaders of several Arab states into growing alignment with Israel -- even as their officials and news media continue to vilify the Jewish state in public.
U.S. officials say Israel's air campaign has played a decisive role in enabling the Egyptian armed forces to gain an upper hand against the militants. But the Israeli role is having some unexpected consequences for the region, including on Middle East peace negotiations, in part by convincing senior Israeli officials that Egypt is now dependent on them even to control its own territory.
Seven current or former British and U.S. officials involved in Middle East policy described the Israeli attacks in Egypt, all speaking on the condition of anonymity to discuss classified information.
Spokesmen for the Israeli and Egyptian militaries declined to comment, and so did a spokesman for the Egyptian Foreign Ministry.
Both neighbors have sought to conceal Israel's role in the airstrikes for fear of a backlash in Egypt, where government officials and the state-controlled media continue to discuss Israel as a nemesis and pledge fidelity to the Palestinian cause.
The Israeli drones are unmarked, and the Israeli jets and helicopters cover up their markings. Some fly circuitous routes to create the impression that they are based in the Egyptian mainland, according to U.S. officials briefed on their operations.
In Israel, military censors restrict public reports of the airstrikes. It is unclear if any Israeli troops or special forces have set foot inside Egyptian borders, which would increase the risk of exposure.
El-Sissi has taken even more care, U.S. officials say, to hide the origin of the strikes from all but a limited circle of military and intelligence officers. The Egyptian government has declared the North Sinai a closed military zone, barring journalists from gathering information there.
Behind the scenes, Egypt's top generals have grown steadily closer to their Israeli counterparts since the signing of the Camp David accords 40 years ago, in 1978. Egyptian security forces have helped Israel enforce restrictions on the flow of goods in and out of the Gaza Strip, the Palestinian territory bordering Egypt controlled by the militant group Hamas. And Egyptian and Israeli intelligence agencies have long shared information about militants on both sides of the border.
Israeli officials were concerned in 2012 when Egypt, after its Arab Spring revolt, elected a leader of the Muslim Brotherhood to the presidency. The new president, Mohammed Morsi, pledged to respect the Camp David agreements. But the Israelis worried about the Muslim Brotherhood's ideological kinship with Hamas and its historic hostility to the Jewish state itself.
A year later, el-Sissi, then the defense minister, ousted Morsi in a military takeover. Israel welcomed the change in government and urged Washington to accept it. That solidified the partnership between the generals on both sides of the border.
The North Sinai, a loosely governed region of mountainous desert between the Suez Canal and the Israeli border, became a refuge for Islamic militants in the decade before el-Sissi took power. The main jihadi organization, Ansar Beit al Maqdis -- the Partisans of Jerusalem -- had concentrated on attacking Israel, but after el-Sissi's takeover it began leading a wave of deadly assaults against Egyptian security forces.
A few weeks after el-Sissi took power, in August 2013, two mysterious explosions killed five suspected militants in a district of the North Sinai not far from the Israeli border. The Associated Press reported that unnamed Egyptian officials had said Israeli drones fired missiles that killed the militants, possibly because of Egyptian warnings of a planned cross-border attack on an Israeli airport. (Israel had closed the airport the previous day.)
El-Sissi's spokesman, Col. Ahmed Ali, denied it. "There is no truth in form or in substance to the existence of any Israeli attacks inside Egyptian territory," he said in a statement at the time, promising an investigation. "The claims of coordination between the Egyptian and Israeli sides in this matter are totally lacking in truth and go against sense and logic."
Israel declined to comment, and the episode was all but forgotten.
Two years later, however, el-Sissi was still struggling to defeat the militants, who by then had killed at least several hundred Egyptian soldiers and policemen.
In November of 2014, Ansar Beit al Maqdis formally declared itself the Sinai province branch of the Islamic State. On July 1, 2015, the militants briefly captured control of a North Sinai town, Sheikh Zuwaid, and retreated only after Egyptian jets and helicopters struck the town, state news agencies said. Then, at the end of October, the militants took down the Russian charter jet, killing all 224 people on board.
It was around that time, in late 2015, that Israel began its wave of airstrikes, the U.S. officials said, which they credit with killing a long roster of militant leaders.
Though equally brutal successors often stepped in to replace them, the militants appeared to adopt less ambitious goals. They no longer dared trying to close roads, set up checkpoints or claim territory. They moved into hitting softer targets like Christians in Sinai, churches in the Nile Valley or other Muslims they view as heretics. In November 2017, the militants killed 311 worshippers at a Sufi mosque in the North Sinai.
Inside the U.S. government, the strikes are widely known enough that diplomats and intelligence officials have discussed them in closed briefings with lawmakers on Capitol Hill, officials said. Lawmakers in open committee hearings have alluded approvingly to the close Egyptian and Israeli cooperation in the North Sinai.
In a telephone interview, Sen. Ben Cardin of Maryland, the ranking Democrat on the Senate Foreign Relations Committee, declined to discuss specifics of Israel's military actions in Egypt, but said Israel was not acting "out of goodness to a neighbor."
"Israel does not want the bad stuff that is happening in the Egyptian Sinai to get into Israel," he said, adding that the Egyptian effort to hide Israel's role from its citizens "is not a new phenomenon."
A former U.S. official described the covert counterterrorism alliance between Israel and Egypt as a "big deal" but said that in recent years, counterterrorism relationships have become "a little bit insulated from ups and downs" of the region's tumultuous politics.
"The public perception of those two countries and how they relate is not in sync with how they work together privately on counterterrorism," said the former official, who was granted anonymity to discuss the sensitive alliance.
Although there was an awareness of the strikes within the U.S. government, the former official said, the United States did not play a significant coordinating or supporting role. The official described the cooperation between Egypt and Israel as "organic."
Egypt, Israel and Hamas broadly began to tighten security cooperation two years ago, forming an unlikely alliance as the Islamic State's offshoot in Sinai began to stage more sophisticated, sustained attacks.
Under pressure from Egypt, Hamas has tightened its border with Sinai over concerns in Cairo that Gaza could be used by Islamic State members as a staging ground. The Islamic State has lost much of its self-declared caliphate in Iraq and Syria over the past three years but remains a threat. Some U.S. counterterrorism experts warn that the group could step up terrorist attacks to prove its relevance, despite the collapse of its armies in Iraq and the loss of Raqqa, its capital in Syria.
U.S. officials have been carefully monitoring some of the group's more significant affiliates, such the branch in Sinai, to see how they may be affected by the broader collapse of the core group.
Information for this article was contributed by David D. Kirkpatrick of The New York Times, and by Greg Jaffe and Loveday Morris of The Washington Post.
A Section on 02/04/2018