Israeli spies had infiltrated deep into Iran’s nuclear and missile programs long before launching recent strikes, conducting years of covert surveillance and gathering detailed intelligence on Tehran’s weapons infrastructure—which was found to be far more advanced and widespread than previously believed.

According to leaked intelligence documents obtained by The Times and shared with Western allies including the U.S. and the UK, the Mossad and other branches of Israeli military intelligence concluded that Iran’s nuclear development extended far beyond the known facilities at Fordow, Natanz, and Isfahan. Their findings suggested a vast and rapidly advancing network of weapons production sites.

An intelligence source told The Times that Israeli operatives had maintained a presence on the ground at multiple key locations for years, with each location having “boots on the ground beforehand.” Preparations for military action reportedly began as early as 2010, in response to intelligence indicating a significant acceleration in Iran’s nuclear ambitions.

Israel’s military operation in Iran targeted three centrifuge production facilities in Tehran and Isfahan—all of which were reportedly destroyed—as well as seven key targets within the Natanz enrichment site. Spies had mapped out overground and underground sections of the facility, identifying piping systems, uranium solidification equipment, and ventilation systems. Additional strikes hit Natanz’s electricity infrastructure, a research and development building, the transformer station, the generator structure to back up the electric grid, and cooling infrastructure.

Beyond Natanz, Israeli spies also infiltrated, attacked, and destroyed the Isfahan site, the Nur and Mogdeh labs, the Shariati military facility, and a hangar at Shahid Meisami where plastic explosives were developed for nuclear testing. Many of these facilities operated under SPND, an Iranian military organization led by nuclear physicist Mohsen Fakhrizadeh, who was assassinated in 2020—allegedly by Israel—using a remote-controlled machine gun.

The documents also revealed that Israel had penetrated the headquarters of the Islamic Revolutionary Guard Corps (IRGC) and attacked additional nuclear sites such as Sanjarian, which was reportedly involved in nuclear weapons component development. By the end of 2024, Israeli intelligence assessed that Iran had transitioned from nuclear research to full-scale weaponization, including advanced explosive systems and radiation-triggered devices—with the potential to assemble a bomb “within weeks.”

The extent and precision of these operations suggest long-term intelligence efforts are still ongoing. “You know they have guys that go in there after the hit, and they said it was total obliteration,” Trump said at a NATO summit in The Hague, implying that Israeli operatives remain active inside Iran.

Evidence of Israel’s deep infiltration dates back to at least 2010, when an Iranian nuclear scientist was assassinated in broad daylight. Since then, four more scientists have been killed. More recently, Hamas leader Ismail Haniyeh was assassinated in Tehran, where Mossad reportedly hired Iranian security personnel to plant explosives in a guesthouse.

The leaked documents also revealed Iran’s goal of producing up to 1,000 long-range surface-to-surface missiles per year, aiming to stockpile 8,000. At the war’s outset, Iran was believed to have between 2,000 and 2,500 ballistic missiles.

Israeli agents had identified and visited nearly every missile-related facility targeted during the recent strikes, which included both military and civilian infrastructure. One of the key sites, Muad Tarkivi Noyad in Rasht—linked to the Iranian Aerospace Industry Organization—manufactured carbon fiber essential for missile production and was destroyed by Israeli bombs.

Dozens of locations were hit during the war including the Parchin military complex southeast of Tehran, as well as centers responsible for missile guidance, navigation, control systems, and warhead and engine manufacturing. The breadth of these attacks exposed a vast, intricate military-industrial network decades in the making.

The intensity of Israel’s operations has heightened paranoia within Iran, where hundreds of people have been arrested in recent days. Following Haniyeh’s assassination, the IRGC launched an aggressive internal crackdown, arresting dozens of individuals on suspicion of espionage. That suspicion was reinforced when Mossad posted a warning on X on Friday advising Iranians to avoid IRGC officials and vehicles.

Mossad’s recruitment tactics remain closely guarded, but the agency’s covert reach has inspired dramatizations such as the popular spy series Tehran. One of its most audacious operations came in 2018, when Mossad agents extracted Iran’s secret nuclear archive from a secure vault—evidence later used to persuade Trump to abandon the 2015 nuclear agreement.

(YWN’s Jerusalem desk is keeping you updated after tzeis ha’Shabbos in Israel)