Four years ago, while Iran's leadership and Revolutionary Guard commanders boasted that Israel would never dare attack the country, Ali Younesi, Minister of Intelligence from 1999 to 2006, .
"The influence of Mossad in various sectors is so extensive that every official of the Islamic Republic should fear for their life. Ignoring Mossad allowed them to infiltrate and strike. Today, we have every reason to be worried about everything," Younesi said at the time.
His warning in 2021 was dismissed and even mocked by some commanders at Iran's Islamic Revolutionary Guard Corps (IRGC)
That same year, : "The highest official in charge of fighting Israeli spies, the one tasked with countering Israeli plots in Iran, turned out to be a spy himself."
And then the 12-day war between Israel, the United States, and Iran showed those warnings were not unfounded.
In the opening hours, four top military commanders and two nuclear scientists tied to Iran's nuclear program were killed by missiles or drones, either at home or during military meetings. By the end of the war, .
The Islamic Republic's official narrative tried to downplay these losses. But two months later, statements from political and security figures, and remarks from families of the dead, revealed the scale of Israel's penetration inside Iran's armed forces and intelligence services.
Shortly after the war, Javad Mansouri, the IRGC's first commander, raised the case of Alireza Akbari, executed in 2023 on charges of spying, . "We had another spy named Akbari who rose to deputy head of the Supreme National Security Council. He was practically running it. Do you think that was just one case?"
Assassination of commanders
The killing of top Iranian commanders in the opening hour showed Israel knew the exact location and meeting place of Iran's highest military officials.
As military leaders and nuclear scientists continued to be targeted, General Gholamreza Jalali Farahani, head of the IRGC's passive defence, . Already under fire for failures during the war, Jalali may have been deflecting blame. But his claim was and rejected by commanders' families.
For her part, the daughter of Major General Ali Shadmani "My father's location changed every few hours. They didn't carry phones or smart devices. Security protocols were followed. Yet, when they moved to a new site, they were immediately targeted. Israel's precise tracking goes beyond WhatsApp or traditional espionage."
On 13 June, after Israel killed the commander of the Khatam al-Anbiya Central Headquarters, Shadmani was appointed to replace him. Four days later, he too was assassinated.
The son of Brigadier General Amir Ali Hajizadeh, commander of the IRGC Aerospace Forces, also dismissed the WhatsApp theory. : "When he wanted to talk, he told us to collect the landline phones and even the TV remote control and move them to another room."
Another case was the killing of Major General Mahmoud Bagheri, commander of the IRGC missile division, known as the "missile engineer." His son later . Bagheri survived those attacks but was killed that same night in a strike on an IRGC meeting.
After these losses, commanders tried holding meetings in non-military sites. Even those were hit.
On 15 June, Tajrish Square in northern Tehran was bombed. One blast destroyed a cultural centre related to the country's Mosques Administration, where senior IRGC and Intelligence Ministry officials had been meeting. IRGC Intelligence Chief Mohammad Kazemi, Quds Force Intelligence Chief Mohsen Bagheri, and their deputies were killed. .
. After the war, Iranian state television aired one such call, in which a voice said to belong to a Mossad agent told an Iranian official: "We are closer to you than your jugular vein."
Attack on the Supreme National Security Council
On 16 June, Israel struck a meeting of the Supreme National Security Council in the basement of a building in western Tehran. The precision of the attack suggested infiltration at the highest level.
Details of the strike emerged only after the war. Even media admitted: "Given the precision of the enemy's information, the possibility of an infiltrator is being investigated."
According to IRGC-linked reports, , targeting not only the meeting room but also emergency exits to block escape routes.
In a recently released , President Masoud Pezeshkian recalled escaping. He said he saw a hole from which air was coming in, and through that, the most high-ranking officials of Iran moved out of the bombed building.
The war offered many examples of Israel's reach. At one point, as he tried to cross into Turkey to negotiate an end to the conflict.
This was not the first time Iran had been penetrated. In 2010, the Stuxnet virus disrupted nuclear facilities. In 2006 and 2009, several nuclear scientists were assassinated. And in 2024, Ismail Haniyeh was killed in a secure zone while meeting Iranian officials.
For years, however, Iranian officials stayed silent or downplayed such incidents. Experts argue this denial only deepened Israel’s influence over Iran’s security system.
Gholamali Jafarzadeh Aymanabadi, a former member of parliament, said infiltration had reached the highest levels of the state. He , mocking the arrests of alleged spies: "Some Mossad spies are looking for Mossad spies among Mossad spies."