Policy Brief By Progress Center for Policies
Introduction:
Despite the buildup of data, reports, and signs suggesting that Israel was preparing an “imminent” strike on Iran, subsequent developments showed that Tehran did not consider these threats serious, dismissing them as mere “intimidation” on the eve of a new negotiation round. The magnitude of the losses—particularly at the leadership level—revealed that Iran was indeed surprised by the seriousness and scale of the Israeli offensive.
Current and Evolving Situation:
On the early morning of June 13, 2025, Israel launched waves of aerial strikes on wide-ranging targets across Iran. Israel declared them to be opening salvos, with additional strikes anticipated over the following days.
The strikes are believed to have aimed at weakening Iran’s military command structure, undermining its ability to retaliate, and destroying—or re-destroying—nuclear and missile facilities.
Air raids targeted air defense sites, military bases, radar systems, and residential buildings. Devastating explosions were reported in densely populated neighborhoods of Tehran.
Precision bombs and drones were reportedly used to assassinate senior military commanders, along with political figures and individuals tied to Iran’s nuclear program.
Most targeted buildings were residential structures in affluent parts of the capital, and casualties are expected to be high—including civilians.
Iranian state media reported the deaths of IRGC Commander-in-Chief Hossein Salami, Khatam al-Anbiya Headquarters Commander Gholam Ali Rashid, and Chief of General Staff Mohammad Bagheri. The fate of Ali Shamkhani, former Supreme National Security Council secretary, remains unclear after his home was targeted.
Habibollah Sayyari, former Navy Commander and Deputy Coordinator of the Iranian Army, was named as interim replacement for Bagheri, while Ahmad Vahidi, former Quds Force commander, replaced Salami.
Two individuals connected to the nuclear program were reported killed: former Atomic Energy Organization head Fereydoon Abbasi and physicist Mohammad Mehdi Tehranchi.
The Natanz nuclear research center, housing thousands of centrifuges, was bombed at least twice and reportedly sustained heavy damage. Israel declared it destroyed.
The assault included a strike on the new Khondab heavy water reactor, and attacks were reported on military sites—including missile bases in Parchin (east of Tehran), and in the cities of Ahvaz, Hamedan, Qom, Qasr-e Shirin, and Tabriz.
Supreme Leader Ali Khamenei stated: “The Zionist entity committed a crime in our beloved country this morning with its blood-stained demonic hands,” condemning the attack on residential areas and promising “harsh punishment by the strong arm of the Iranian armed forces.” He acknowledged the deaths of several leaders and scientists, saying their successors would carry on without delay.
Iran’s Foreign Ministry accused Israel of acting with U.S. coordination and approval, declaring Washington “responsible for the serious consequences of this recklessness.”
Observers noted that the Israeli strike extended beyond Iran’s nuclear program, targeting the very core of the Islamic Republic’s regime by hitting the IRGC command structure.
Despite the high-level assassinations, senior political figures—especially Khamenei—have not yet been directly targeted. Analysts suggest Washington needs fresh decisions from the Iranian leadership to accommodate the new balance of power.
Iranian sources acknowledged Tehran was caught off guard and had not taken measures to protect its military leadership, believing an Israeli strike unlikely.
Even after warnings from Washington—including President Donald Trump’s own statement about a possible “imminent” Israeli strike—Iran dismissed it all as bluffing.
The announcement of the sixth round of U.S.-Iranian negotiations in Muscat on June 15 may have misled Tehran into thinking military action was off the table.
Analysts expect Iran to retaliate, likely targeting Israeli—not American—assets, despite Tehran having declared that any Israeli aggression would be considered American aggression.
Military sources suggest Iran currently lacks the capacity to mount a credible retaliatory strike, especially as Trump publicly announced U.S. readiness to defend Israel.
Hezbollah in Lebanon is not expected to act in solidarity with Iran. Lebanon’s government reportedly asked the group not to drag the country into war, stating that Lebanon would not allow itself to be involved in a conflict that does not concern it.
Negotiations between Iran and the U.S. are expected to be delayed, resuming only after Israel completes its military objectives and Tehran absorbs the shock.
Experts believe the Israeli strike has reshuffled the diplomatic deck: now, not just Iran’s nuclear program, but the nature of its regime is in question.
U.S. sources maintain that Washington still hopes to return to negotiations. President Trump reaffirmed this after the strike. Iran, however, has not confirmed whether its Foreign Minister Abbas Araghchi will attend the upcoming Muscat talks.
It is believed Trump authorized or greenlit the Israeli attack during a June 9 phone call with Netanyahu.
Summary:
Strategic Surprise for Iran:
Despite repeated warnings of an Israeli strike, Tehran treated them as mere negotiation tactics, exposing a failure in intelligence assessment. Some believe the announcement of the June 15 Muscat negotiation session reinforced Tehran’s misreading of the threat. Conversely, others argue it was a deliberate ploy—possibly aided by Washington—to ensure Israel’s surprise attack.
Shift in Israeli Targeting:
By hitting top military leaders and residential areas in the capital, Israel has signaled that it is targeting the Iranian regime’s internal balance of power—not just its nuclear capabilities.
Limited Iranian Response Expected:
Given its eroded deterrent capabilities and desire to avoid open conflict with the U.S., Iran is unlikely to pursue a full-scale response.
Military Pressure as a Negotiation Tool:
Washington appears to have resorted to military escalation to gain leverage in upcoming talks with Iran.
Anticipated Political Recommendations:
Upgrade Iran’s intelligence assessment capabilities to better detect and interpret hostile intentions, and reconsider leadership appointments based on military competence rather than ideological loyalty to maintain cohesion.
Iran’s response should be limited and focused on Israeli targets to avoid escalating into a broader confrontation with the U.S. or its allies.
Re-enter negotiations in Muscat (if held), recognizing that Iran’s negotiating position has weakened—necessitating greater flexibility in exchange for concrete guarantees.
Improve ties with neighboring countries to reduce international isolation and strengthen domestic resilience.
Reorganize the nuclear file by shifting control away from the IRGC and placing it under civilian scientific authorities to complicate future targeting efforts.
