He arrived in Cairo a few months earlier to conduct research for his doctorate at Cambridge. Raised in a small village near Trieste by a sales manager father and a schoolteacher mother, Regeni, a 28-year-old leftist, was enthralled by the revolutionary spirit of the Arab Spring. In 2011, when demonstrations erupted in Tahrir Square, leading to the ouster of President Hosni Mubarak, he was finishing a degree in Arabic and politics at Leeds University. He was in Cairo in 2013, working as an intern at a United Nations agency, when a second wave of protests led the military to oust Egypt’s newly elected president, the Islamist Mohamed Morsi, and put Sisi in charge. Like many Egyptians who had grown hostile to Morsi’s overreaching government, Regeni approved of this development. ‘‘It’s part of the revolutionary process,’’ he wrote an English friend, Bernard Goyder, in early August. Then, less than two weeks later, Sisi’s security forces killed 800 Morsi supporters in a single day, the worst state-sponsored massacre in Egypt’s history. It was the beginning of a long spiral of repression. Regeni soon left for England, where he started work for Oxford Analytica, a business-research firm.

From afar, Regeni followed Sisi’s government closely. He wrote reports on North Africa, analyzing political and economic trends, and after a year had saved enough money to start on his doctorate in development studies at Cambridge. He decided to focus on Egypt’s independent unions, whose series of unprecedented strikes, starting in 2006, had primed the public for the revolt against Mubarak; now, with the Arab Spring in tatters, Regeni saw the unions as a fragile hope for Egypt’s battered democracy. After 2011 their numbers exploded, multiplying from four to thousands. There were unions for everything: butchers and theater attendants, well diggers and miners, gas-bill collectors and extras in the trashy TV soap operas that played during the holy month of Ramadan. There was even an Independent Trade Union for Dwarfs. Guided by his supervisor, a noted Egyptian academic at Cambridge who had written critically of Sisi, Regeni chose to study the street vendors — young men from distant villages who scratched out a living on the sidewalks of Cairo. Regeni plunged into their world, hoping to assess their union’s potential to drive political and social change.

But by 2015 that kind of cultural immersion, long favored by budding Arabists, was no longer easy. A pall of suspicion had fallen over Cairo. The press had been muzzled, lawyers and journalists were regularly harassed and informants filled Cairo’s downtown cafes. The police raided the office where Regeni conducted interviews; wild tales of foreign conspiracies regularly aired on government TV channels.

Regeni was undeterred. Proficient in five languages, he was insatiably curious and exuded a low-intensity charm that attracted a wide circle of friends. From 12 to 14, he served as youth mayor of his hometown, Fiumicello. He prided himself on his ability to navigate different cultures, and he relished Cairo’s unruly street life: the smoky cafes, the endless hustle, the candy-colored party boats that plied the Nile at night. He registered as a visiting scholar at American University in Cairo and found a room in Dokki, a traffic-choked neighborhood between the Pyramids and the Nile, where he shared an apartment with two young professionals: Juliane Schoki, who taught German, and Mohamed El Sayad, a lawyer at one of Cairo’s oldest law firms. Dokki was an unfashionable address, but it was just two subway stops from downtown Cairo with its maze of cheap hotels, dive bars and crumbling apartment blocks encircling Tahrir Square. Regeni soon befriended writers and artists and practiced his Arabic at Abou Tarek, a four-story neon-lit emporium that is Cairo’s most famous spot for koshary, the traditional Egyptian dish of rice, lentils and pasta.

He spent hours interviewing street vendors in Heliopolis and at the small market behind the Ramses train station. To win their trust, he ate from the same grubby street carts as his subjects; his academic supervisor at American University warned he would get food poisoning. Regeni didn’t care: He glided through Cairo with a quiet sense of purpose.

By chance, Valeriia Vitynska, a Ukrainian he met in Berlin four years earlier, had come to Cairo for work. They reconnected. ‘‘She was more beautiful than I remembered,’’ he texted a friend. They took a trip to the Red Sea, and when she returned to her job in Kiev, they kept the relationship going over Skype. ‘‘It was very intense and beautiful,’’ Regeni’s friend Paz Zárate told me. ‘‘He was so joyful, so full of hope for the future.’’

Yet Regeni was also conscious of Cairo’s dangers. ‘‘It’s very depressing,’’ he wrote Goyder a month into his stay. ‘‘Everyone is superaware of the games that are going on.’’ In December he attended a meeting of trade-union activists in central Cairo and wrote about it, under a pseudonym, for a small Italian news service. During the meeting, he told friends, he spotted a veiled young woman taking his picture with her cellphone. It was disconcerting. Regeni complained to friends that some street vendors were hassling him for favors, like new cellphones. Then his relationship with his main contact, a burly man in his 40s named Mohamed Abdullah, took a strange turn.

Abdullah, who worked for a decade for a Cairo tabloid, in distribution, before rising to the top of the street vendors’ union, was Regeni’s guide, offering advice and introducing him to men he could interview. One evening in early January last year, the two met in an ahua — a cafe where men often smoke water pipes — near the Ramses train station. Over tea, they discussed a £10,000 ‘‘scholar activist’’ grant offered by a British nonprofit group called the Antipode Foundation. Regeni offered to apply for the money. Abdullah had other ideas. Could it be used for ‘‘freedom projects’’ — political activism against the Egyptian government? No, it could not, Regeni replied firmly. Abdullah changed tack. His daughter required surgery, and his wife had cancer. He would ‘‘jump on anything’’ for cash. Regeni, growing exasperated, gesticulated theatrically as he touched the limits of his Arabic. ‘‘Mish mumkin,’’ he said. It’s not possible. ‘‘Mish professional.’’

Two weeks later, on the fifth anniversary of the 2011 uprising, Cairo was in lockdown. Tahrir Square was deserted except for 100 or so government supporters bused in to wave Sisi signs and take selfies with the riot police. The security services had been rounding up potential protesters for weeks, raiding downtown apartments and cafes. Like most Cairenes, Regeni spent the day at home, working and listening to music. Once darkness fell he deemed it safe to leave the apartment: An Italian friend had invited him to a birthday party for an Egyptian leftist. They’d arranged to meet at a cafe near Tahrir Square.

Before heading out, Regeni listened to a Coldplay song — ‘‘A Rush of Blood to the Head’’ — and texted Vitynska. ‘‘I’m going out,’’ he announced at 7:41 p.m. It was a short walk to the subway. But by 8:18 Regeni still had not arrived. His Italian friend began trying to contact him — at first with texts, then with frantic calls.

Among the most intoxicating promises of the Arab Spring was the hope that Egypt’s detested security apparatus would be dismantled. In March 2011, in the heady early months of the uprising, Egyptians stormed the headquarters of State Security, the chief arm of Mubarak-era repression, and emerged with lists of informants, copies of surveillance photos and transcripts of intercepted phone calls. Some found pictures of themselves. There were calls for a radical overhaul of the security sector. But as the country skidded into post-revolution disorder, the talk of reform was lost. After Sisi came to power, in 2013, it became clear how little had changed.

State Security was renamed the National Security Agency, but it remained under the control of the powerful Interior Ministry, which was thought to employ at least 1.5 million police officers, security agents and informants. Officers who had been fired were reinstated and the torture chambers reopened. Opposition leaders, fearing arrest, fled the country. Human rights monitors started to count the numbers of the ‘‘disappeared’’ — critics who vanished into state custody without arrest or trial — until the monitors, too, began to disappear.

Today, Egypt is arguably a harsher place than it ever was under Mubarak. After seizing power, Sisi was elected president in 2014 with 97 percent of the vote. Parliament is stuffed with his supporters, and the jails are filled with his opponents — 40,000 people, by most counts, primarily from the banned Muslim Brotherhood, the Islamist organization founded in 1928, but also lawyers, journalists and aid workers. Sisi justifies these measures by pointing to the danger from extremists. Islamic State militants have been fighting Egyptian soldiers in Sinai since 2014; this year they sent suicide bombers into Coptic churches, killing dozens. A good number of Egyptians worry that without a firm hand, their nation of 93 million could become the next Syria, Libya or Iraq. Most of the country’s elites, fearing the kind of upheaval that followed the Arab Spring, are firmly with Sisi; many of its intellectuals, dismayed by their short-lived experiment with democracy, admit that they are out of ideas.

Unaffiliated with a political party, Sisi draws his authority from the totems of the state — generals, judges and security chiefs — who are increasingly powerful. The guiding principle of this incipient police state is to prevent a recurrence of the events of 2011, one Western ambassador, who asked to remain unnamed because he is not authorized to speak on the subject, told me as we sat in his garden last winter. In his final decade in power, Mubarak made a number of concessions. The Muslim Brotherhood won a fifth of the seats in Parliament; the press enjoyed a measure of freedom; some labor strikes were grudgingly permitted. But none of this saved Mubarak — in fact, in the view of Sisi officials, his laxity hastened his demise. The lesson was clear: ‘‘To give an inch is a mistake,’’ the ambassador said, listing the characteristics of the Sisi regime, ‘‘secrecy, paranoia, the sense that you assert power by looking strong and not showing weakness or building bridges.’’

Deciphering the inner workings of the three major security agencies has become a fixation of Egypt watchers. ‘‘It’s very opaque, like a black box,’’ Michael Wahid Hanna of the Century Foundation, a policy institute based in New York, told me. ‘‘But there are clues.’’

The security agencies are loyal to Sisi, Hanna explained, but are always jockeying for position. National Security, thought to have 100,000 employees and at least as many informants, remains the most visible. Its emergent rival is Military Intelligence, which traditionally steered clear of politics but has expanded under Sisi, who led the agency from 2010 to 2012. The General Intelligence Service is Egypt’s equivalent of the C.I.A. Hugely powerful under Mubarak, it is now viewed as somewhat diminished.

Together, these agencies enjoy inordinate influence. They own TV stations, control blocs in Parliament and dabble in business; their agents patrol the streets and the internet. They draw the red lines in Egyptian society between what is permissible and what is not. That makes Egypt a perilous place to navigate for critics: One wrong move, or even a misjudged joke (Egyptians have been jailed for their Facebook posts), can lead to imprisonment or to being barred from leaving the country. Amnesty International puts the number of disappeared at 1,700 and says that extrajudicial executions are common.

When Regeni arrived in 2015, foreigners were thought to be subject to different rules. It was true that some had run into trouble. Earlier that year, the Australian journalist Peter Greste of Al Jazeera was finally freed after 13 months in jail on charges of ‘‘damaging national security’’; a French student was expelled for interviewing democracy activists. Regeni’s academic advisers warned him to avoid contact with members of the Muslim Brotherhood. ‘‘The situation here is not easy,’’ he messaged a friend a month after he arrived. But on the whole, Regeni, his supervisor later told me, believed that his passport would protect him. His abiding fear was that he would be sent back to Cambridge before he could finish his research.

A week after Regeni vanished, Italy’s ambassador to Cairo, Maurizio Massari, was seized by a sense of foreboding. With his shock of gray hair and his polished charm, Massari was a popular fixture on the Cairo diplomatic circuit. He liked to host gatherings of Egyptian academics and politicians, and on weekends he watched soccer games with his American counterpart, Ambassador R. Stephen Beecroft. Now, he restlessly paced the long marble corridors of the Italian Embassy overlooking the Nile.

News of Regeni’s disappearance was rippling across Cairo. His friends had started an online search campaign with the hashtag #whereis­giulio. Regeni’s parents had flown in from Italy and were staying at his apartment in Dokki. A rumor circulated that Regeni had been snatched by Islamist radicals — a terrifying prospect because, six months earlier, a Croatian engineer kidnapped on the outskirts of Cairo was beheaded by Islamic State militants. The ambassador’s anxiety was amplified by the response of Egyptian officials. The Italian intelligence station at the embassy had no leads, so he sought out the foreign minister, the minister of military production and Sisi’s national-security adviser Fayza Abul Naga. All claimed to know nothing of Regeni. The most disquieting encounter was with the powerful interior minister, Magdi Abdel-Ghaffar, who took six days to agree to a meeting only to sit impassively as the Italian diplomat pleaded for help. Massari left perplexed: Abdel-Ghaffar, a 40-year veteran of the security services, had an army of informants on the streets of Cairo. How could he be in the dark?

The police started a missing-persons investigation but seemed to be pursuing some odd lines of inquiry. When detectives interviewed Amr, a leftist university professor and a friend of Regeni’s who asked that his last name not be used to protect him from retaliation, they repeatedly asked if Regeni was gay. ‘‘I told them he has a girlfriend,’’ Amr said when we met over coffee near his home in the suburb of Maadi. ‘‘Then the next guy goes: ‘Are you sure he is straight? Maybe he’s one of these bisexuals.’ ’’

‘‘I said, ‘You should just find him.’ ’’

The crisis was compounded by the arrival of a high-level Italian trade delegation. Since 1914, Italy had maintained diplomatic ties with Egypt, embracing the country even when others kept their distance. Italy was Egypt’s biggest trading partner in Europe — nearly $6 billion in 2015 — and Rome prided itself on its close ties to Cairo. In 2014 Matteo Renzi, then the Italian prime minister, became the first Western leader to welcome Sisi in his capital, and Italy continued to sell weapons and surveillance systems to Egypt even as evidence of rights abuses mounted.

The day after Massari’s meeting with the interior minister, Italy’s investment minister, Federica Guidi, flew to Cairo with 30 Italian executives, hoping to strike deals in construction, energy and the arms trade. Now Regeni was at the top of the agenda. The group went straight to Al-­Ittihadiya, the main presidential palace, where months earlier, Regeni had helped the street vendors during the police raid outside its back gates. Massari and Guidi were ushered into a private meeting with Sisi, who listened gravely as the Italians outlined their concerns. But he, too, offered only sympathy.

That evening Massari hosted a reception for the trade delegation and Egyptian business leaders at the embassy. About 200 people mingled in the reception hall, sipping wine as they waited for dinner to be served. Among them was Egypt’s deputy foreign minister, Hossam Zaki, who pushed through the crowd to Massari, wearing a dark expression. ‘‘Don’t you know?’’ he said.

‘‘Know what?’’ Massari replied.

‘‘A body has been found.’’

Early that morning, the driver of a passenger bus traveling the busy Alexandria Desert Highway, in western Cairo, noticed something on the side of the road. When he got out, he discovered a body, naked from the waist down and smeared in blood. It was Regeni.

Massari rushed to the Four Seasons hotel, where Guidi was staying, and together they phoned Renzi and the foreign minister, Paolo Gentiloni. They canceled the reception, sending puzzled guests home without explanation. Then Massari and the minister went to Regeni’s apartment in Dokki, where Regeni’s parents were staying. When the ambassador embraced Regeni’s mother, Paola Deffendi, her worst fears were confirmed. ‘‘It’s all over,’’ she later told the press. ‘‘The happiness of our family was so short.’’

Massari arrived at the Zeinhom morgue in central Cairo after midnight. A small team from the embassy, including a policeman, accompanied him. At first, morgue officials refused them entry. ‘‘Open the door!’’ yelled Massari, visibly agitated. Massari was finally led into a chilled room where Regeni’s body was laid out on a metal tray.

Regeni’s mouth was agape and his hair was matted with blood. One of his front teeth was missing and several were chipped or broken, as if they had been struck with a blunt object. Cigarette burns pocked his skin, and there were a number of deep wounds on his back. His right earlobe had been sliced off, and the bones in his wrists, shoulders and feet were shattered. A wave of nausea washed over Massari. Regeni appeared to have been extensively tortured. Days later, an Italian autopsy would confirm the extent of his injuries: Regeni had been beaten, burned, stabbed and probably flogged on the soles of his feet over a period of four days. He died when his neck was snapped.

The office of Ahmed Nagy, the prosecutor who initially oversaw Regeni’s murder investigation, is on the seventh floor of the dilapidated Giza courthouse building, a few miles from Tahrir Square. On any given day, hundreds of people course through the narrow corridors — lawyers, manacled prisoners and their families. When I went to see him a few weeks after Regeni’s death, Nagy, a wiry chain-smoker, was perched behind a Louis XIV-style desk piled with papers and half-drunk cups of coffee.

In the early hours of the investigation, Nagy spoke with astonishing bluntness. He told reporters that Regeni suffered a ‘‘slow death’’ and allowed that the police might be involved: ‘‘We don’t rule it out.’’ But soon after that, the chief detective on the case suggested that Regeni died in a car crash. Lurid theories appeared in the papers and on TV: Regeni was gay and had been murdered by a jealous lover. He was a drug addict or a Muslim Brotherhood pawn. He was a spy. Several reports noted his work at Oxford Analytica, which had been founded by a one-time Nixon administration official, as a probable sign of employment by the C.I.A. or Britain’s M.I.6. At a news conference, the interior minister, Abdel-Ghaffar, dismissed suggestions that the security forces had detained Regeni. ‘‘Of course not!’’ he said. ‘‘This is the final say in the matter: It did not happen.’’

Nagy’s office was cool and dark, the blinds tightly drawn as air spewed from a noisy air-conditioning unit. With his slicked-back hair and flickering smile, Nagy affected an air of easy confidence. But the boldness he once demonstrated about the Regeni case was gone. He responded to my questions with polished evasions, lighting one cigarette after another as he spoke. ‘‘Murders can go unsolved,’’ Nagy concluded after 30 unfruitful minutes. ‘‘We will just have to wait. Inshallah, something will come of it.’’

Egyptian officials have a long record of facing crises in just this way: denial, then obfuscation, followed by running the clock in hopes that the problem will fade away. In September 2015, the month Regeni arrived, an Egyptian helicopter gunship shot dead eight Mexican tourists and four Egyptians as they picnicked in the Western Desert, having mistaken them for terrorists. Instead of apologizing, the authorities tried to blame the tour guides, then promised an investigation that has never reported any findings. The government of Mexico was furious. A month later, Egypt initially refused to admit that an Islamic State bomb had downed a Russian jetliner over Sinai, killing 224 people, even though both Russia and the Islamic State said it had.

But if Egyptian officials thought they could bluff their way out of the Regeni crisis, they miscalculated. More than 3,000 people attended his funeral in his home village, Fiumicello; across Italy, grief turned to outrage as details emerged of his agonizing torture. In the press, Regeni was often portrayed in a photo that showed him smiling with a cat in his arms. Yellow banners with the slogan Verità per Giulio Regeniappeared in cities and villages. ‘‘We will stop only when we find out the truth,’’ Renzi, the prime minister, told reporters. ‘‘The real truth, and not a convenient truth.’’

Renzi’s fury was based on more than a hunch. In the weeks after Regeni’s death, the United States acquired explosive intelligence from Egypt: proof that Egyptian security officials had abducted, tortured and killed Regeni. ‘‘We had incontrovertible evidence of official Egyptian responsibility,’’ an Obama administration official — one of three former officials who confirmed the intelligence — told me. ‘‘There was no doubt.’’ At the recommendation of the State Department and the White House, the United States passed this conclusion to the Renzi government. But to avoid identifying the source, the Americans did not share the raw intelligence, nor did they say which security agency they believed was behind Regeni’s death. ‘‘It was not clear who gave the order to abduct and, presumably, kill him,’’ another former official said. What the Americans knew for certain, they told the Italians, was that Egypt’s leadership was fully aware of the circumstances around Regeni’s death. ‘‘We had no doubt that this was known by the very top,’’ said the other official. ‘‘I don’t know if they had responsibility. But they knew. They knew.’’

Weeks later, in early 2016, John F. Kerry, then secretary of state, confronted Egypt’s foreign minister, Sameh Shoukry, during a meeting in Washington. It was a ‘‘pretty contentious’’ conversation, one Obama official told me, although the Kerry team couldn’t figure out if Shoukry was stonewalling or simply didn’t know the truth. The blunt approach ‘‘raised eyebrows’’ inside the administration, another said, because Kerry had a reputation for treating Egypt, a fulcrum of American foreign policy since the 1979 Egypt-­Israeli peace treaty, with kid gloves.

By then a team of seven Italian investigators had arrived in Cairo to help with the Egyptian investigation. They were hindered at every turn. Witnesses appeared to have been coached. Surveillance footage from the subway station near Regeni’s apartment had been deleted; requests for metadata from millions of phone calls were refused on the grounds that it would compromise the constitutional rights of Egyptian citizens. Some brave Egyptian witnesses visited the investigators at their temporary office in the basement of the Italian Embassy. But even there the Italians were uneasy.

Massari, the ambassador, became concerned about embassy security after Regeni’s death; soon he stopped using email and the phone for sensitive matters, resorting to an old-fashioned paper-based encryption machine to send messages to Rome. Italian officials worried that Egyptians who worked in the Italian Embassy were passing information to Egyptian security forces; they noticed that the lights were permanently off in an apartment across from the embassy — a good spot to place a directional microphone. Massari, still traumatized by the memory of Regeni’s injuries, had become a recluse, avoiding meetings with other ambassadors. His relationship with the Egyptian government was deteriorating; Egyptian officials, infuriated by an interview he gave to an Italian TV station, determined that he was trying to pin the murder on them. ‘‘We deduced he had already taken sides,’’ Hossam Zaki, the deputy foreign minister, told me later. ‘‘He was kind of moot. Useless.’’ When Massari did venture out, people noted that he looked exhausted. Friends said he was struggling to sleep.

International pressure was building on the Egyptians. Italian newspapers sent their most dogged investigative reporters to Cairo. A website called RegeniLeaks sprang up, soliciting tips from Egyptian whistle-blowers. Regeni’s mother began her own campaign to uncover the truth, relating in a news conference that she was able to recognize his battered body only by ‘‘the tip of his nose.’’ Italian actors, TV personalities and soccer players rallied to her side. Egyptians told Deffendi that her son had ‘‘died like an Egyptian’’ — a badge of honor in Sisi’s Egypt. The European Parliament passed a stinging resolution condemning the suspicious circumstances under which Regeni had died; in London, campaigners presented a petition with more than 10,000 signatures to Parliament, calling for the British government to ensure a ‘‘credible investigation.’’ The F.B.I. was also assisting in the Italian investigation; when an Egyptian friend of Regeni’s landed in the United States, on vacation, agents pulled her aside for an interview.

This time stonewalling wasn’t going to work. ‘‘We are in deep [expletive],’’ observed a leading TV host, Amr Adeeb, on his show.

‘‘Do you speak Latin?’’ Luigi Manconi, an Italian senator who championed the Regeni family’s cause, asked when I visited him in Rome in January. ‘‘There is a phrase in Latin — arcana imperii. It means the secrets of power.’’

He paused and looked up for effect.

‘‘That is what we see in Egypt: the dark side of those institutions; the secrets in their hearts.’’

The senator was referring to Egypt’s security agencies, but what he didn’t mention was that the Regeni investigation was also exposing painful rifts inside the Italian state. There were other priorities. Italy’s intelligence services needed Egypt’s help in countering the Islamic State, managing the conflict in Libya and monitoring the flood of migrants across the Mediterranean. And Italy’s state-controlled energy company, Ente Nazionale Idrocarburi, or Eni, had its own stake. Weeks before Regeni arrived in Cairo, Eni announced a major discovery: the Zohr gas field, 120 miles off the north coast of Egypt, which contained an estimated 850 billion cubic meters of gas — the equivalent of 5.5 billion barrels of oil.

Italy is one of Europe’s most energy-vulnerable countries, which makes Eni more than just a $58 billion titan with operations in 73 countries; it makes it an integral part of Italian foreign policy. In 2014, Renzi acknowledged as much, calling Eni ‘‘a fundamental piece of our energy policy, our foreign policy and our intelligence policy.’’ In many countries, Eni’s chief executive Claudio Descalzi — a towering Milanese oilman, who has driven recent exploration efforts across Africa — knows the leaders better than Italy’s ministers do.

As the pressure to solve Regeni’s murder mounted, Descalzi, a regular visitor to Cairo, assured Amnesty International that the Egyptian authorities were ‘‘putting in maximum effort’’ to find Regeni’s killers. He discussed the case at least three times with Sisi. According to one official at Italy’s Foreign Ministry, diplomats came to believe that Eni had joined forces with Italy’s intelligence service in a bid to find a speedy resolution to the case. Eni has a long history of hiring retired Italian spies to staff its internal security division, says Andrea Greco, a co-author of ‘‘The Parallel State,’’ a 2016 year book on Eni. ‘‘They have a strong collaboration,’’ he said. ‘‘I’m sure they may have collaborated in the Regeni case, although it’s not for certain that their interests are aligned.’’ A spokeswoman for Eni says that the company was ‘‘horrified’’ by Regeni’s death and while it had no responsibility to investigate, it continued ‘‘to follow the matter very closely’’ in its interactions with the Egyptian government.

The perceived cooperation between Eni and Italy’s intelligence services became a source of tension inside the Italian government. Foreign Ministry and intelligence officials turned guarded with one another, sometimes withholding information. ‘‘We were at war, and not only with the Egyptians,’’ one official told me. Diplomats suspected that Italian spies, in an attempt to close the case, had brokered an interview by the Italian newspaper La Repubblica with Sisi six weeks after Regeni’s death. (The editor of La Repubblica maintains that the request for the interview came from the newspaper.) In it, Sisi sympathized with Regeni’s parents, calling his death ‘‘terrifying and unacceptable,’’ and vowed to find the culprits. ‘‘We will get to the truth,’’ he said.

On March 24, eight days after the interview appeared, the Cairo police opened fire on a minivan carrying five men, several with criminal records or histories of drug abuse, as it drove through a well-to-do suburb. All five were killed, and the police issued a statement calling them a gang of kidnappers who had been targeting foreigners. In a subsequent raid on an apartment linked to the men, the police said they discovered Regeni’s passport, credit card and student identity card. Soon, state media was reporting that Regeni’s killers had been identified. The Italian investigators, who were at the Cairo airport to fly home for Easter, were recalled, and the Interior Ministry thanked them for their cooperation.

In Italy, news of the shooting met with skepticism — the hashtag #noncicredo, I don’t believe it, circulated on Twitter. The Egyptian account quickly fell apart. Witnesses told several journalists (including me) that the men had been executed in cold blood. One was shot as he ran, his corpse later positioned inside the van. ‘‘They never stood a chance,’’ one man told me, shaking his head. The men’s link to Regeni crumbled: Italian investigators used phone records to show that the supposed gang leader, Tarek Abdel Fattah, was 60 miles north of Cairo the day he supposedly kidnapped Regeni.

Last fall, Egypt’s chief prosecutor told his Italian counterpart that two police officers had been charged with murder in connection with the five deaths. But an awkward question remained: If the dead men hadn’t killed Regeni, then how did his passport get into their apartment?

Italians had little doubt that the whole episode was a crude cover-up, so badly bungled that the Egyptians had incriminated themselves. Yet it had worked. The Italian detectives left Cairo, and the investigation stalled. Massari was replaced with a new ambassador who was ordered to remain in Rome. In Egypt, ‘‘Regeni’’ became a word to be whispered. ‘‘Everyone who cares about Giulio is afraid,’’ Hoda Kamel, a union organizer who helped Regeni in his research, told me. ‘‘It feels like all of the state, with all of its strength, is trying to kill the story.’’

After months of strained diplomatic ties, the Egyptian wall of denial cracked — or seemed to. In a trip to Rome last September, Egypt’s chief prosecutor, Nabil Sadek, publicly admitted that Egypt’s National Security Agency, suspecting Regeni of espionage, had been monitoring him. In a series of meetings over the next few months, he provided the Italians with documents — phone records, witness statements and a video — that showed Regeni was betrayed by several people close to him.

Muhammad Abdullah, Regeni’s contact in the street vendors’ union, was an informant for the National Security Agency. Using a hidden camera, he had taped his conversation with Regeni about the £10,000 grant (the Egyptians handed over the video). He made a statement detailing his meetings with his handler, Col. Sharif Magdi Ibrahim Abdlaal, who, he said, had promised him a reward once the Regeni case was closed.

The identity of the second person was perhaps more surprising. Italian officials came to believe that in the month before Regeni vanished, his lawyer roommate, Mohamed El Sayad, allowed officials from the National Security Agency to search the apartment. In the weeks that followed, phone records showed, Sayad spoke with two National Security Agency officials.

Sayad did not respond to requests for comment, but I had a long exchange, over Facebook, with Regeni’s other roommate, Juliane Schoki. Her account was symptomatic of the climate of mistrust in Sisi’s Cairo. According to Schoki, Sayad voiced suspicions of Regeni within days of his moving into their flat. ‘‘I think Giulio is a spy,’’ she recalled him saying.

After Regeni disappeared, she began to share that view. The two speculated that he was working for Mossad. (Regeni, she said, told her he once had an Israeli girlfriend and had visited Israel.) Schoki, who has since left Egypt, relayed this theory to Egyptian intelligence officers. ‘‘They were surprised because they had the same idea,’’ she recalled.

After Regeni died, she would sit with Sayad watching thrillers on TV, saying, ‘‘That’s exactly how it is!’’ — something that, in retrospect, ‘‘looks a bit ridiculous,’’ she admitted. ‘‘But a year ago it made perfect sense.’’

The Italians used Egyptian phone records to make other connections and discovered that the police officer who claimed to have found Regeni’s passport had been in touch with members of the National Security team that had been following Regeni. Suddenly, Regeni’s parents dared to hope the truth might surface. ‘‘The evil is unraveling slowly, like a ball of wool,’’ his parents wrote in a letter published in La Repubblica on the first anniversary of his disappearance.

But although the Egyptians admitted to surveilling Regeni, they insisted they had not abducted or killed him. And even if that could be proved, the core mystery remained: Why had he been ‘‘killed like an Egyptian’’? One common theory pointed to the work of a rogue officer. At the Interior Ministry, which controls National Security, even low-level officers enjoy considerable autonomy yet are rarely held to account, according to Yezid Sayigh, a senior associate at the Carnegie Middle East Center in Beirut. ‘‘Things may happen that Sisi does not approve of,’’ he said. But there was much else that made little sense. Which Egyptian official figured that torturing a foreigner was a good idea? Why dump his body on a busy highway, instead of burying it in the desert where it might never be found? And why produce his body as a high-level Italian delegation arrived in Cairo?

An anonymous letter sent to the Italian Embassy in Bern, Switzerland, last year and later published in an Italian newspaper, offered another explanation: Regeni had been caught in a shadowy turf war between National Security and Military Intelligence, with one group seeking to use his death to embarrass the other. The details suggested that the author of the account was intimately familiar with Egypt’s security apparatus, yet it also seemed improbable that one person could know so much. Senior American officials told me the letter was consistent, however, with broader intelligence reports of the fierce jockeying for power among rival security agencies. ‘‘They try to use cases as a lever to embarrass one another,’’ one said.

The most alarming possibility is that Regeni’s death was a deliberate message — a sign that, under Sisi, even a Westerner could be subjected to the most brutal excesses. In Rome, an official told me that when Regeni’s body was discovered, it was propped up against a wall. ‘‘Did they want him to be found?’’ the official asked. The Obama official said he believed that someone in the ‘‘upper echelons’’ of the Egyptian government may have ordered Regeni’s death ‘‘to send a message to other foreigners and foreign governments to stop playing with Egypt’s security.’’

No senior Egyptian official agreed to speak to me for this article. But Hossam Zaki, the former deputy foreign minister who is now assistant secretary general at the Arab League, told me that Egyptian officials believe that the murder was the work of an unidentified ‘‘third party’’ seeking to sabotage Egypt’s relations with Italy. ‘‘Egyptians do not treat foreigners badly, full stop,’’ he said.

Nonetheless, Regeni’s death cast a chill over Cairo’s shrinking expatriate community. ‘‘Few things have shaken me so deeply,’’ one European diplomat told me. Before we spoke, the diplomat asked me to deposit my cellphone in a signal-blocking box so that our conversation could not be surveilled. Regeni’s death, the diplomat continued, signaled Egypt’s broader direction: Regeni had fallen victim to the paranoia about foreigners that now coursed through Egyptian society; since the revolution, even small interactions could be fraught. During lunch in Cairo’s Islamic Quarter, the diplomat recounted, an agitated man remonstrated loudly with another guest for taking a photo of a meal — beans, bread and tamiyya, the Egyptian falafel. ‘‘He started to shout: ‘You’re a foreigner. You will use this image to show that we only eat beans and bread!’ ’’

In Fiumicello, where Regeni grew up and his parents still live, a banner reading ‘‘Verità per Giulio Regeni’’ hangs in the main church, but few believe that the truth will ever come out. Regeni’s family has closed ranks, appointing a pugnacious lawyer as its gatekeeper, and begun their own investigation into his murder. (His parents declined to be interviewed for this article but answered some questions by email.) At the Rome headquarters of the Carabinieri’s Special Operations Group, which specializes in counterterrorism and anti-mafia operations, Gen. Giuseppe Governale insists that there is still hope of solving the crime. ‘‘The Arab mentality is to procrastinate until everyone forgets,’’ he said. ‘‘But we will not stop until we find an answer. We owe it to his mother.’’

Italians have what Carlo Bonini, a journalist for La Repubblica who has written extensively on the Regeni case, calls ‘‘the last bullet.’’ Under Italian law, they could press charges in an Italian court against the handful of Egyptian security officials they believe to be responsible. But that might be a Pyrrhic victory: Egypt would never extradite anyone for trial. And there seems little chance that Sisi can be pressured into revealing the truth. In Rome last month officials admitted that the investigation was now little more than geopolitical kabuki; politics and not police work would determine its conclusion. In the 18 months since Regeni was killed, Sisi has had dinner with the German chancellor, Angela Merkel, in front of the pyramids, and in April he received a rapturous welcome at the White House from President Trump. On Aug. 14, the Italian government announced it intended to send its ambassador back to Cairo. The Zohr gas field is on track to start production in December.

In Fiumicello, Regeni lies buried under a line of cypress trees. Flowers, devotional candles and plastic-wrapped volumes of Spinoza and Hesse are piled on his grave, and a small photograph shows him speaking to a crowd, clutching a microphone, his face open and earnest. But unlike the elaborate neighboring tombs that surround it, Regeni’s gravestone is just a plain marble slab. Because the investigation is still open, the parish priest explained, officials might yet need to exhume his remains.