Israel targets Iran’s nuclear sites and senior military figures

In a joint operation led by the Israeli Defense Forces (IDF) and the Mossad, Israel’s foreign intelligence agency, Israel targeted Iran’s nuclear and military infrastructure and key leaders. The attack, reported by some sources to involve as many as 300 airstrikes, began overnight on June 12 and continued into June 13. Strikes targeted the Natanz and Fordow nuclear facilities as well as senior commanders of the Islamic Revolutionary Guard Corps (IRGC) and Iran’s Armed Forces.

Israel attacked hours after the International Atomic Energy Agency’s (IAEA) Board of Governors declared Iran in breach of its non-proliferation obligations on June 12. In retaliation against the nuclear watchdog’s resolution, the Tehran regime announced plans to construct a new enrichment facility “in a secure location,” violating the IAEA’s modified Code 3.1. IAEA Director General Rafael Grossi had warned on June 9 that Iran’s lack of transparency prevents the verification of a peaceful program.

On the diplomatic front, negotiations between the US and Iran had reached an impasse in recent rounds, with both sides unable to bridge the divide over uranium enrichment. Washington insisted on full dismantlement, while Tehran declared such a demand a red line. Iranian Supreme Leader Ali Khamenei consistently expressed deep skepticism toward talks with the United States, echoing a longstanding US distrust that spanned both the current and previous US administrations.

US Secretary of State Marco Rubio issued a statement shortly after the strikes commenced, describing Israel’s moves as “unilateral action” and cautioning Tehran against retaliating against the United States. “We are not involved in strikes against Iran, and our top priority is protecting American forces in the region,” Rubio said. “Let me be clear: Iran should not target U.S. interests or personnel.”

Iran’s nuclear sites

The central focus of Israel’s military campaign appears to be the Natanz and Fordow nuclear facilities, each critical to Iran’s uranium enrichment program but distinct in design and vulnerability. Natanz is a sprawling complex with above- and below-ground components primarily housing Iran’s IR-1 and IR-2 centrifuges. Fordow, in contrast, is deeply buried within a mountain near Qom and designed to withstand heavy bombardment, making it far harder to attack.

Israel reportedly struck Natanz first—multiple times—on June 12, followed by an attack on Fordow early on June 13. While it was long assumed that Israel would need US-supplied bunker-busting munitions delivered by B-2 or B-52 bombers to effectively strike such hardened sites, the current campaign suggests Israel is acting unilaterally. This situation raises questions about the extent of damage Israel inflicted and its ability to sustain strikes against deeply fortified targets.

Videos circulating on social media also show kinetic engagement in Tehran’s Amir Abad neighborhood, where the headquarters of the Atomic Energy Organization of Iran is located.

Military leaders and nuclear scientists eliminated

The first attack wave also targeted key IRGC and Islamic Republic of Iran Armed Forces personnel, and anonymous sources told Reuters that Israel had eliminated at least 20 “Iranian commanders.” Khamenei was quick to reappoint successors for some of these key posts. Among the individuals reported killed are:

• IRGC member and Armed Forces Chief of Staff Major General Mohammad Bagheri, who harmonized the relations between the IRGC and Iran’s conventional army, known as Artesh. Bagheri is succeeded by the former Army (Artesh) Commander Seyyed Abdolrahim Mousavi.
• Ali Shamkhani, the advisor to the Supreme Leader, an Expediency Discernment Council member, and the former Supreme National Security Council secretary, who was reportedly tasked with handling the nuclear file behind the scenes.  
• IRGC Commander Major General Hossein Salami. He is succeeded by the former IRGC Ground Forces commander, Mohammad Pakpour.
• IRGC Aerospace Force Commander Brigadier General Amir Ali Hajizadeh, who led the regime’s ballistic missile program.
• IRGC Khatam-al Anbiya Central Headquarters (KCHQ) Commander Gholam Ali Rashid. KCHQ is the highest operational military command in Iran, responsible for the planning, coordination, and operational oversight of the armed forces. Rashid is succeeded by the former KCHQ Coordination Deputy Commander Ali Shademani.

Notably, there are conflicting reports about the fate of Esmail Ghaani, the commander of the IRGC’s Quds Force who is responsible for the regime’s extraterritorial operations. His status is unclear as of this writing.

Iranian state media outlets have confirmed the deaths of six Iranian nuclear scientists—Abdolhamid Minoochehr, Ahmadreza Zolfaghari, Seyed Amir Hossein Faghahi, Akbar Motalebizadeh, Mohammad Mehdi Tehranchi, and Fereydoon Abbasi-Davani—who were reportedly assassinated.

Among them, Tehranchi was president of Islamic Azad University and a nuclear physicist; Minoochehr and Zolfaghari were experts in reactor design and nuclear simulation; Faghahi previously served as deputy head of the Atomic Energy Organization; and Abbasi-Davani was its former director.

In addition to these confirmed casualties, some reports claim that six other nuclear weapons scientists—Saide Borji, Mansour Askari, Ahmad Haghighat Talab, Seyed Mohammad Reza Sadighi Saber, Ali Foolsdvand, and Ali Bakouei Katrimi—were also killed.

On June 13, as Israel’s large-scale assault on Iran persisted, Israeli National Security Advisor Tzachi Hanegbi told Channel 12, “We currently have no plans to kill Khamenei and his people.”

Air defense systems, military bases, and ballistic missile stockpiles targeted

The Mossad released footage showing its operations inside Iran on the morning of June 13, including a video of two covert agents launching missiles from within the country. An Israeli official said the agency had established a hidden drone base in Iran to carry out the strikes, which targeted ballistic missile launchers near Tehran to prevent retaliation during Israel’s broader military campaign. Israeli forces also smuggled weapon systems into Iran to neutralize air defenses, securing air superiority. In a separate operation, Mossad commandos deployed precision missiles near anti-aircraft sites in central Iran.

An Israeli official told Iran International that Israel successfully thwarted the launch of hundreds of Iranian surface-to-surface missiles. The operation neutralized truck convoys carrying missiles and disrupted one of Iran’s most sensitive military systems. Using front companies, smuggled components, and intelligence gathered over time, the Mossad remotely activated the operation from nearly 2,000 kilometers away. At the Spadjabad base near Tehran, explosive drones—deployed and activated by trained operatives—disabled missile launchers. In a separate operation, precision-guided missiles smuggled into Iran struck air defense sites around Tehran.

IDF published a video highlighting the different targets, categorized as military leaders, nuclear sites, air defense systems, surface-to-surface missiles, and nuclear scientists. A separate statement added that dozens of launchers, storage sites for surface-to-surface missiles and drones, as well as other military sites, were destroyed in the attacks. At one of the sites attacked in western Iran, a unique launch mechanism housed inside containers was installed.

Another Persian-language IDF post on X mentioned that the following models of the regime’s air defense system were also destroyed: SA-63 (105 km range), SA-96 (an S-300 copy, 300km range), SA-68 (85 km range), and SA-71 (24km range).

Iranian sources are also claiming that the Imam Ali missile site, located in Khorram Abad in Lorestan Province, was targeted.

Israel also reportedly struck airbases in Tabriz City, East Azerbaijan Province, and Hamedan City, Hamedan Province, where the regime stations its F-4 Phantom II fighter jets.

Iran follows through on threats of retaliation

Iranian Supreme Leader Ali Khamenei, President Masoud Pezeshkian, and new Armed Forces Chief of Staff Mousavian vowed to retaliate against Israel, while Iran’s Foreign Ministry declared that it holds the United States responsible for the Israeli strikes.

IRGC-affiliated outlets claimed that ballistic missiles were launched toward central and northern Israel, with some reportedly reaching Tel Aviv. US forces have assisted in intercepting incoming projectiles—mirroring the joint defense posture seen during the Iranian missile barrage of October 2024.

Janatan Sayeh is a research analyst at the Foundation for Defense of Democracies focused on Iranian domestic affairs and the Islamic Republic’s regional malign influence.