Gen. Abdullah Saberi, an Iranian commander, stepped out for a jog early one morning in an upscale diplomatic quarter of Syria’s capital. Israeli intelligence officers waited nearby. Posing as movers, they had slipped past the neighborhood’s security checkpoints.

As he headed for a nearby park, General Saberi passed two men who carried an oversize refrigerator box. In a flash, the men restrained the general, drugged him, threw the box over his head, shoved him into a white van and left as if nothing had happened.

He was whisked to Israel for interrogation, according to numerous officials in the Middle East, including senior Iranian officials close to General Saberi and a Syrian official who reviewed video of the September 2021 kidnapping.

As a veteran of Iran’s powerful Islamic Revolutionary Guards Corps, General Saberi knew many secrets. But his interrogators were interested in only one.

What did he know about Ron Arad?

Mr. Arad, an Israeli airman, vanished decades ago, and the Israeli military says he is the only service member classified as missing in action. The government’s long search for him has captivated the public and has come to symbolize Israel’s commitment, rooted in Jewish tradition, to bringing its soldiers home, dead or alive. Articles, books and documentaries have been produced about the hunt for Mr. Arad.

The Israeli government was so determined to find him that, even four decades after his disappearance, it took the risk of kidnapping General Saberi in the shadow of his own embassy.

Mr. Arad was the only thing that interrogators asked him about, Iranian officials said.

General Saberi’s abduction and interrogation, details of which have not previously been reported, were particularly remarkable because several Israeli intelligence reports had concluded, over many years, that Iran had not been involved in Mr. Arad’s disappearance.

Yet time and again, a New York Times investigation found, Israeli intelligence officials gave greater credence to reports and assumptions that Iran must be to blame for the airman’s disappearance or knew about his whereabouts. That belief, which officials said was genuinely held, justified cross-border raids, kidnappings, harsh interrogations and more.

The Times investigation also discovered something else: the answer to one of the region’s enduring spy mysteries, the two-decade-old disappearance of an Iranian general, Alireza Asgari. In hunting for Mr. Arad, Israeli officials kidnapped the general, interrogated him about Mr. Arad and then killed him. He had no intelligence on Mr. Arad.

“It was a collective blind spot,” said Avi Kalo, a retired senior Israeli military officer who wrote a detailed report in 2016 that, like others, found no conclusive evidence of Iranian involvement. Yet operations against Iran continued.

“Iran,” Mr. Kalo said, “was the boogeyman.”

Today in Israel, after years of bloody operations targeting Iran, the prevailing thinking among people involved with the hunt for Mr. Arad is that he was never held by Iran, and that Tehran was not involved in his disappearance, officials familiar with the intelligence told The Times. Recent information collected during Israel’s wars with Iran and Hezbollah has only hardened that conclusion.

Officials who were once certain that Iran was responsible told The Times that they had most likely been wrong all along, including Raz Zimmt, a former Israeli military intelligence analyst who helped write a key 2005 report that pointed blame at Tehran. That assessment, he said in a recent interview, was probably mistaken because of “a natural inclination to pin everything on the regime in Tehran.”

In interviews, nobody suggested that Israeli intelligence officials had intentionally misled the government over the decades about Iran’s role. Rather, they said that the conclusions were based on fragmented or circumstantial evidence and were probably influenced by confirmation bias — the tendency to give more weight to conclusions that fit with previously held beliefs.

Such biases have clouded Israel’s vision before. Before the Oct. 7, 2023, Hamas-led attacks on Israel, officials were preoccupied by Iran and Hezbollah and underestimated the closer threat posed by Hamas, even as it raised millions and prepared for an assault. Israeli officials were so convinced that Hamas could not muster a coordinated attack that they doubted it despite obtaining the battle plans.

Israeli officials were again overconfident in their intelligence before the current war with Iran, when they incorrectly predicted a popular uprising that could topple the government in Tehran.

Israel’s foreign intelligence service, the Mossad, declined to comment on the intelligence that it had produced on Mr. Arad and the operations that it carried out to find him. A spokeswoman for the Israeli military said that Mr. Arad was regarded as alive and missing in action.

The Times interviewed dozens of Iranian, Israeli and American officials and others directly involved in the hunt for Mr. Arad. The Times also interviewed families, friends and associates of the two abducted Iranian generals. Some spoke on the condition of anonymity to discuss military and intelligence secrets.

These interviews reveal new details about key moments, faulty assumptions and fatal costs. The hunt for Mr. Arad is, in its own way, a story of generations of mutual mistrust and violence between Israel, Iran and its proxies. The fighting and secret diplomacy have spanned nearly the entire history of the Islamic Republic of Iran. Israeli leaders, no matter their political parties, have relied on intelligence to hold Iran responsible for Mr. Arad’s disappearance.

In one indication of how the thinking has changed, Israeli commandos set out this year in the hopes of finding Mr. Arad’s body — not in Iran, but in a small Lebanese village.

That is where the saga began.

Disappearance

On Oct. 16, 1986, an Israeli F4-Phantom jet streaked through the sky over southern Lebanon. Mr. Arad, then a 28-year-old weapons officer, took aim at a Palestine Liberation Organization target and fired.

The bomb detonated prematurely, badly damaging the aircraft. Mr. Arad ejected.

Everyone agrees, after years of investigations, that Mr. Arad was captured by a Lebanese Shiite militia and political group known as Amal. The group’s chief of security, Mustafa Dirani, took charge of the fallen airman.

The militants offered to trade their hostage for millions of dollars and the release of Palestinian and Lebanese prisoners. But Israel’s defense minister at the time, Yitzhak Rabin, had suffered politically for a prisoner swap in 1985 and was reluctant to make a deal.

As progress stalled on locating Mr. Arad, Israeli suspicion fell on Iran and its Shiite Islamic government. It was a reasonable assumption. Iran was a major player in Lebanese politics and provided training and money to Shiite groups, including Amal.

In 1989, Mr. Arad’s wife announced that the Israeli government had told her that it had “irrevocable proof” that her husband was alive and that he had been handed over to Iranian operatives.

Iranian involvement in Mr. Arad’s disappearance quickly became conventional wisdom, despite Israeli officials’ making no progress in locating him in Iran.

An Iranian Doctor With a Story

The Iran theory got a major boost in 1992 inside the Mossad.

Israel Perlov, a veteran officer, figured that Mr. Arad most likely would have been wounded in his fall and would have needed medical care. Mr. Perlov set out looking for doctors who might have seen the airman.

He found an Iranian doctor who claimed to have treated Mr. Arad in both Tehran and Lebanon. This was potentially a breakthrough moment. If the doctor were credible, it would be solid evidence that Mr. Arad had indeed been taken to Iran.

But a polygraph test produced inconclusive results on the question of Iran. So Mr. Perlov tested the doctor a second time. Again, the test showed signs of “disturbances” when the doctor described seeing Mr. Arad in Iran.

“But they were not significant enough to negate the veracity of his response,” Mr. Perlov wrote in a book released last year.

He found the doctor credible, but decided to put the doctor to the test. Mr. Perlov opened a suitcase full of cash and offered it as a reward. All the doctor had to do was prove that he had treated the missing airman.

He never saw the doctor again, and Mossad agents never corroborated his story. But Mr. Perlov wrote that his encounters with the doctor bolstered the idea that the “Iranians were up to their necks in holding Ron.”

A few years later, another Mossad officer, Rami Igra, would review this encounter and come to a very different conclusion.

In his view, Mr. Igra told The Times, the doctor was a liar who had been angling for a big payday. Mr. Igra suspected that the Mossad had gone looking for proof of its own assumption, and found it.

But the doctor’s story became part of the official evidence against Iran. Mr. Igra’s contrarian assessment gained little traction.

Operation Poisonous Sting

The most explosive evidence against Iran burst into public view in 1994, and it shaped public opinion and news accounts for decades.

Israeli commandos stormed into Lebanon and kidnapped Mr. Dirani, the militia member who was last known to have held Mr. Arad. They whisked him to an underground prison in an operation known as Poisonous Sting.

Under questioning, Mr. Dirani said he had stashed Mr. Arad in a home in the Lebanese village of Nabi Chit, where a trusted family could watch him. One night, he said, the men assigned to guard Mr. Arad had left the house, probably in response to an unrelated Israeli raid nearby. When they returned, he said, Mr. Arad was gone.

Years had passed, and Mr. Dirani said he did not know where the airman was.

Mr. Dirani’s interrogator did not believe that.

“You couldn’t reason with Dirani. The only thing that worked was force,” the interrogator, Doron Zehavi, later recalled in an interview.

Mr. Dirani would later testify that he was physically and sexually tortured — claims that the Israeli government broadly denied. But it acknowledged rough treatment and that Mr. Dirani may have been threatened with sexual assault.

Under harsh interrogation, Mr. Dirani recounted a meeting with an Iranian official who told him that the Revolutionary Guards had snatched Mr. Arad and taken him to an Iranian prison camp.

“After his soul was drained out, when he spat blood, then he tells us about a massive Revolutionary Guards camp complex in Iran,” Mr. Zehavi said.

Some believed this as incriminating evidence against the Iranians. Others regarded it as coerced and too unreliable to act on. Mr. Igra, the Mossad officer, concluded that there was no evidence that Iranian officials had held Mr. Arad.

To date, no evidence has surfaced to prove Mr. Dirani’s account of Mr. Arad’s being held in an Iranian prison, officials say. Some officials believe that Mr. Dirani had honestly recounted his conversation with the Iranian official, but that the information itself was bad.

Mr. Igra’s analysis did not conclude what had happened to Mr. Arad. Maybe he had been killed while trying to escape. Perhaps his captors had executed him as revenge in the tit-for-tat fighting that had defined the era.

The most logical explanation, he assessed, was that Mr. Arad’s story began and ended in Lebanon. “It was a simple solution to a complex problem,” Mr. Igra said.

But Mr. Dirani’s story was big news in Israel. It seemed to confirm years of suspicions that Iran was behind Mr. Arad’s disappearance. Journalists, analysts and top government officials repeated it for years.

“The Iranian authorities have been holding Ron Arad for more than six years,” Mr. Rabin said in 1995, “and they are directly and fully responsible for his fate.”

Iran Joins the Hunt

Convinced that Iran was to blame, the Israeli government put intense pressure on government leaders in Tehran.

“The issue of Ron Arad followed us everywhere,” Mohammad Ali Abtahi, Iran’s vice president from 1997 to 2005, told The Times in a telephone interview from Tehran. “In every international encounter we had, we were asked about Ron Arad, Ron Arad.”

The case even followed them to the Vatican. When the Iranian president at the time, Mohammad Khatami, visited Rome in 1999, Pope John Paul II presented him with a letter from Mr. Arad’s wife, pleading for information, Mr. Abtahi recalled.

“Israel was obsessed about Iran’s role in the Ron Arad case,” he said. “Our position was that this has nothing to do with us. It happened in Lebanon.”

Something about that gnawed at some Israeli intelligence officials. Iran knew that Israel would pay a hefty price for information about Mr. Arad. If Iranian leaders possessed such information, why would they not try to capitalize on it?

Finally, in 2004, it seemed like that might happen.

Israel agreed to free a high-profile Lebanese inmate in exchange for genetic evidence proving what happened to Mr. Arad. Hezbollah’s leader at the time, Hassan Nasrallah, was eager to make that happen, so he enlisted help from the Iranian government.

“I got the impression that they — Hezbollah and the Iranians — were truly trying with all their might to locate the body,” Gerhard Conrad, a German intelligence officer who helped mediate the negotiations, told The Times. “Nasrallah knew he could extract any price for him, even if he was dead.”

Iran dispatched Abdullah Saberi, a Revolutionary Guards commander who’d served many years in Lebanon, to help coordinate the search, according to former Israeli and Iranian officials.

The Hezbollah-Iranian investigation concluded with a secret report saying that Mr. Arad had died in 1988 in Nabi Chit, the village in eastern Lebanon where he had been held, according to three former Iranian officials. The document, the details of which have not been previously reported, concluded that he was most likely buried somewhere there.

The findings were considered so important that the former president of Iran Ali Akbar Hashemi Rafsanjani, who was involved in the search, dispatched one of his children to Germany to hand-deliver them.

“During the entire negotiations, Israel was insisting that we find information on Ron Arad, but we couldn’t find anything,” said Hossein Mousavian, a former Iranian ambassador to Germany.

The German mediators saw such high-level engagement as a sign of Iran’s seriousness and willingness to engage.

Israel read it completely differently.

Why, intelligence officers asked, would Iran have dispatched a Revolutionary Guards commander to lead the search if it had not been involved with the disappearance? To the Israelis, this was evidence of high-level Iranian complicity.

“The fact that a highly important Iranian general flew to Lebanon from Tehran to bring a unique body of knowledge and help Hezbollah locate the grave only added to our deep conviction that Iran was behind this event,” Mr. Zimmt, the former intelligence officer who participated in the review, told The Times.

Israel’s 2005 report that concluded that Mr. Arad must have been kidnapped by the Revolutionary Guards. (This landmark report remains classified, but its conclusion has been widely reported.)

Mr. Zimmt, today a highly regarded scholar who studies Iran, said that looking back, he and his colleagues had gotten tunnel vision. “And it wouldn’t be the last time,” he said.

A Killing, Despite Warnings

In 2006, Yuval Diskin, the head of Israel’s domestic security agency, Shin Bet, launched a comprehensive review of the Arad case. After two decades without a breakthrough, investigators re-examined every aspect.

“We went through everything, item by item, and examined all the sources, their reliability and the way the information had been obtained,” Mr. Diskin told The Times in an interview. “We reached the conclusion that all the reports or analyses based on those reports, according to which Ron Arad had been transferred to or had reached Iran at some stage, were incorrect and were based on serious mistakes in reading the intelligence that had been collected, or on unreliable or erroneous information.”

This intelligence assessment was reported earlier by the Israeli journalist Yoav Limor in his 2023 book, “The Interrogator.”

The Shin Bet team concluded that Mr. Arad never fell into the hands of Hezbollah or the Revolutionary Guards. The answer to his disappearance, the team said, most likely rested in the village of Nabi Chit — the very place that the Hezbollah-Iranian investigation had pointed to.

That report got little traction inside the government, Mr. Diskin said

Rather than dropping the Iran theory, the Mossad doubled down with an audacious, and previously unreported, kidnapping operation.

A general in the Quds Force of the Revolutionary Guards named Alireza Asgari had been on the Mossad’s radar for years. The general had close ties with Hezbollah leaders and had risen to be deputy Iranian defense minister. Most important, he had arrived in Lebanon shortly after Mr. Arad vanished.

In December 2006, General Asgari flew to Istanbul and checked into the Ceylan Hotel, according to his wife, Ziba Ahmadi. From there, he vanished.

General Asgari’s disappearance quickly became one of the intelligence world’s biggest whodunits.

The Israelis have steadfastly denied involvement.

Years later, as the United States and Iran negotiated a nuclear deal and prisoner swaps, the Iranians asked their American counterparts what had happened to their missing general. American officials denied involvement, but quietly began asking questions themselves.

Israeli officials told U.S. negotiators that General Asgari was dead, according to a former American official involved in the negotiations. Three other former American officials who worked closely with Israel said that Mossad operatives kidnapped him, interrogated him for weeks and killed him.

One of the former officials said that General Asgari had been questioned aboard a boat and dumped into the Black Sea. They said that the Mossad had questioned the general over potential involvement in Mr. Arad’s disappearance. Interrogators had found no such ties.

In an interview with The Times, Yitzhak Ilan, a top Shin Bet investigator, recalled a discussion with Mossad officials before General Asgari’s disappearance. Though he did not name the general, he said he had been briefed on a risky intelligence mission related to the airman’s disappearance.

“I understood, even before the operation, that the solution was not there at all,” he told The Times before his death in 2020.

It is not clear how much the Americans told Iran about what they had learned about General Asgari’s disappearance. Iran conducted its own investigation, and Ms. Ahmadi told The Times that investigators had told her that Israeli operatives had entered her husband’s hotel room, drugged him and kidnapped him.

She said that investigators had found the vehicle used in the operation abandoned by the Black Sea.

Asked why the Israelis would want to question her husband, she replied, “Have you ever heard of Ron Arad?”

More Warnings. Another Abduction.

General Asgari’s interrogation had failed to turn up evidence of Mr. Arad’s whereabouts. So once again, officials started from scratch.

Mr. Kalo, who led the Israeli military’s missing-in-action unit in 2014, recounted in an interview with The Times how he had examined years of intercepted communications, informant reports and analytical assessments.

He reached the same conclusion that the Shin Bet team and the Hezbollah-Iranian investigation had reached years earlier. Mr. Arad had most likely died in 1988, probably in Nabi Chit. He was never in Iran.

Mr. Kalo said he delivered his lengthy report to Prime Minister Benjamin Netanyahu of Israel in late 2016. The conclusion quickly appeared on Israel’s Channel 2 news.

By the time Mr. Kalo retired in 2019, he thought the Iran theory had been laid to rest. In discussions with his colleagues, he recommended focusing future intelligence-gathering on Nabi Chit.

Mr. Kalo said he made clear to Israeli intelligence officers that abducting Iranians would not solve the Arad case.

But two years later, nearly two decades after he helped coordinate the Hezbollah search for Mr. Arad in Lebanon, General Saberi stepped out of his apartment and ended up inside a refrigerator box and a Mossad moving van.

The Israelis never stopped suspecting that General Saberi must know something about the airman’s whereabouts.

After a lengthy interrogation, the dazed general was dumped on a street in Johannesburg, South Africa. He later said he was tortured.

As questions swirled in Israel, David Barnea, the Mossad chief at the time, said he had authorized an operation to find information on Mr. Arad. He described the mission as “courageous and daring,” but ultimately a “failure.”

A Return to the Beginning, at Last

After that, Mr. Barnea told Mossad members that they might as well throw everything they knew about the Arad case into the shredder, associates recall.

None of the operations, the abductions, the raids or the killings had gotten them closer to finding this missing airman. The Mossad began looking seriously at Nabi Chit.

This was the village, Mr. Dirani had told interrogators long ago, where he had stashed Mr. Arad in the care of a trusted family. Those friends had left Mr. Arad alone one night, he had said, to fight Israeli troops nearby.

It is also the village that the Hezbollah-Iranian investigation had identified as Mr. Arad’s probable resting place. At least two subsequent Israeli inquiries had reached the same conclusion.

One of the few men suspected of knowing Mr. Arad’s location back in 1988, former Israeli and current Lebanese officials said, was Ahmad Shukr, a retired Lebanese security officer. Last December, Mr. Shukr left home for a meeting about what he thought was a business deal.

He promptly disappeared, and Lebanese officials believe that he was abducted by Israeli agents. Mr. Shukr’s whereabouts remains a mystery, as does what he may have told investigators.

Israeli officials now say that the closest thing the government has to a theory is that Mr. Arad was executed as retribution for the killing of Mr. Shukr’s brother, who died battling Israeli forces that night in 1988. (Ahmad Shukr’s niece Rana Shukr said in an interview that her uncle had nothing to do with Mr. Arad.)

A few months after Mr. Shukr’s disappearance, Israeli soldiers descended on Nabi Chit in one of the deadliest clashes of this latest round of fighting with Hezbollah. Dozens of Lebanese were killed and wounded.

Israeli soldiers searched a corner of a cemetery, looking for the remains of Mr. Arad, and unearthed a grave. They found nothing, but officials say that the search continues — with a focus now on Lebanon rather than Iran.

“We should have gone there 20 years ago. It was a failure,” Mr. Kalo said. “We could not get away from the narrative that Iran was involved. We could not untie Arad from the threat of Iran. It was too deeply rooted in our obsession.”

Gal Koplewitz and Euan Ward contributed reporting.