Iranian Nuclear Question and Israel’s Threat Perceptions

Summary

Despite US and Israeli strikes on Iranian nuclear sites, most estimates note that the Iranian nuclear capabilites have remained largely intact. The future of the Iranian nuclear programme, meanwhile, remains uncertain with Iran suspending cooperation with the International Atomic Energy Agency.

Introduction

The Israel Defense Forces (IDF), in the early hours of 13 June 2025,  launched an air offensive against the Iranian nuclear programme and missile bases.[1] The military strikes, dubbed as a ‘preemptive’ operation, also targeted Iranian airfields and naval bases.[2] In response to the military strikes, Iran launched a barrage of missiles targeting major Israeli cities. What followed was a 12-day conflict that inflicted heavy casualties and material damage on both sides, while also leading to the closure of regional airspace. The US later joined the operation on 22 June with limited strikes on Iran’s nuclear sites, particularly the underground Fordo facility, before extending a helping hand to facilitate a fragile ceasefire between Iran and Israel.[3]

Since the beginning of the strikes against Iran and its nuclear facilities, Tehran has repeatedly threatened to withdraw from the nuclear non-proliferation treaty (NPT). In this regard, Iranian Parliament suspended cooperation with the International Atomic Eenrgy Agency (IAEA), in effect, making it difficult for the agency to verify Iranian complaince under its NPT obligations. In the absence of IAEA’s oversight on Iranian nuclear programme, analysts flag the possibilities of additional military strikes on Iranian nuclear facilities as well as an Iranian nuclear breakout. Both of these possibilites pose a serious threat to regional peace and seucrity.

Overview of the 12-Day War

Decades of Israeli warnings against the Iranian nuclear programme culminated in what Prime Minister Benjamin Netanyahu dubbed as ‘Operation Rising Lion’. In remarks after the strikes, he claimed that the operation targeted the “heart of Iran’s nuclear enrichment programme”.[4] The urgency to strike was based on the IDF’s assessment of an imminent threat posed by Iran reaching the nuclear threshold and the rapid expansion of its ballistic missile capabilities.[5]

Operationally, Iran suffered a significant setback in the initial strikes, as Israel successfully managed to eliminate several of the Islamic Republic’s top nuclear scientists along with high-ranking military and Islamic Revolutionary Guard Corps (IRGC) commanders in a coordinated operation.[6] Days after the launch of the operation and US bombers targeting Iranian nuclear facilities, Tehran launched a missile attack on the US air base in Qatar.[7] By the time the ceasefire took effect, both Israel and Iran had sustained heavy damage. While Israel reported 28 casualties, Iran suffered a significantly heavier toll, with the number of casualties exceeding 900.[8]

Iranian Nuclear Programme

The Iranian nuclear programme began in the late 1950s with the close cooperation of the United States, France and Germany, for the supply of enriched fuels, nuclear power reactors as well as uranium enrichment plants.[9] In order to build a solid institutional foundation for Tehran’s nuclear modernisation, the Atomic Energy Organisation of Iran (AEOI) was established in 1974 and nuclear scientists were sent for training abroad.[10] Interestingly, it was Iran under the Shah regime which proposed making the entire West Asian region a nuclear weapons free zone.[11] Although the nuclear programme came to a grinding halt with the Islamic revolution of 1979,[12] it restarted in the mid-1980s during the Iran–Iraq war. As the western nuclear suppliers confronted a hostile regime in Iran, they withdrew their support to Iran forcing Tehran to turn towards Soviet Union and China. In 1994, Russia agreed to construct Bushehr nuclear power plant as Iran’s first civilian nuclear reactor.[13]

The regional security landscape in West Asia since the Islamic revolution of 1979 has been complicated for Iran, a factor driving Tehran’s nuclear ambitions. On Iran’s western side, Saddam Hussein’s Iraq and on the eastern side significant presence of the Taliban in Afghanistan presented an acute security threat to Tehran. In the first half of the 2000s, the United States gained political and military presence over both these countries, further making the region hostile for Iranian security.

Amidst a hostile regional landscape, Iran’s nuclear programme became the centre of gravity for the international community. The concerns over militarisation of Iran’s nuclear programme have been raised for over three decades when the Central Intelligence Agency estimated in 1992 that Iran was seeking nuclear weapons.[14] The IAEA in 2003 highlighted Iran’s infringement on its NPT commitments.[15] The concerns were related to Iranian lack of clarification on particles of Highly Enriched Uranium (HEU) discovered at a number of Iranian nuclear facilities.[16] Following the production of Uranium Hexafluoride at Isfahan facility in August 2005, IAEA finally decided to refer Iran’s case to the United Nations Security Council (UNSC).

In April 2006, as Iran declared it had achieved uranium enrichment to about 3.5 per cent at its Natanz pilot enrichment plant, Western powers followed a dual approach. On the one hand, they proposed a framework agreement offering incentives to halt its enrichment programme (under the P5[17]+1 format) in June 2006, on the other hand, the UNSC adopted resolution 1696 mandating Iran to suspend its enrichment programme.[18] Over the next few years, more sanctions were imposed on Tehran while diplomatic negotiations were also underway.

The negotiations between Iran and the US witnessed a fundamental shift when Obama Administration came to power. The P5+1 and Iran agreed on a proposal where Iran would export most of its 3.5 per cent enriched uranium in return for 20 per cent enriched uranium fuel for the Tehran Research Reactor. However, the agreement fell apart due to domestic opposition in Iran, prompting the UNSC to adopt Resolution 1929 in 2010, significantly expanding the sanctions.[19]

During a tough negotiation phase marked by contestation over Iranian right to enrich uranium and lifting of Western sanctions on Tehran, Prime Minister Netanyahu in the United Nations General Assembly in 2012 advocated for a clear red line on Iranian nuclear programme.  He stated that Iran’s “enrichment facilities are the only nuclear installations that we can definitely see and credibly target”.[20] Negotiations over the next three years ultimately led to an agreement between Iran and P5+1 termed as the Joint Comprehensive Plan of Action (JCPOA) in July 2015. Ahead of the agreement, in March 2015, Netanyahu speaking before the joint meeting of US Congress, asserted that the deal being negotiated with Iran was a “bad deal” as it did not take away the Islamic Republic’s ability to ultimately obtain nuclear weapons.[21] Among other provisions, the deal sought to reduce Iranian uranium enrichment capacity to only 3.67 per cent (that too only at Natanz) for 15 years. In return, both the US and the UN agreed to temporarily halt most of the sanctions.

The years of negotiations over a nuclear deal between Iran and the Western powers came crashing down when President Donald Trump unilaterally withdrew from the JCPOA in May 2018 citing its inability to protect America’s security interests.[22] This decision was welcomed by Netanyahu as “bold”.[23]  In April 2021, Iran declared its intention to enrich uranium to 60 per cent U-235 as a response to a sabotage attempt of its vast underground enrichment cascades at Natanz.[24] In the latest round of attacks by Israel, the IAEA has clarified that although electricity infrastructure including an electrical sub-station, a main electric power supply building, and emergency power supply and back-up generators were destroyed in Natanz, there has been no substantial damage on the underground cascade hall containing part of the Pilot Fuel Enrichment Plant and the main Fuel Enrichment Plant.[25]

Israel’s Threat Perception and Security Strategy

Over the years, Iran has developed the most sophisticated, largest and diverse ballistic and cruise missile capabilities (see Table 1).[26] During the Iran–Iraq war, Iran’s ballistic missile requirements were largely met by foreign suppliers like Libya, Syria and North Korea in the form of Scud class missiles. Shahab class missiles (Iranian name of Scud class missiles) lacked the requisite range to target Tehran’s foes like Israel and western part of Saudi Arabia. In the early 2000s, Iran modified these missiles to improve their range (1,600 km) and performance and named it Ghadr-1. In a significant enhancement of Iran’s missile capabilities, Tehran unveiled its first hypersonic missile Fattah 1 with a speed up to Mach 15 and a range of up to 1,400 km.

Threat perceptions tend to influence security behaviours and decisions, which are fundamentally based on security awareness of leadership and state capabilities. Whether alarming or real, Israel’s understanding of Iran’s nuclear and ballistic missile programme has been time and again articulated by its political and military leadership. Israel’s perception of geopolitical environment is profoundly shaped by its strategic culture, which is the cumulative expression of its collective memory, rooted in persecution and a persistent sense of existential threat.[27] For Israeli leaders, ever since the 1979 Iranian revolution, the Islamic Republic has been an arch rival, obsessed with Israel’s destruction. Public statements by Iranian Supreme Leader Ayatollah Ali Khamenei, calling Israel a “cancerous tumor to be destroyed”[28] alongside the financing and arming of Israel’s non-state adversaries, have exacerbated Israel’s security concerns.[29]

Despite the absence of any formally adopted national security doctrine or strategy, certain fundamental principles have guided Israel’s national security over the years. These principles have been formulated and often reshaped with geopolitical shifts. Some of these are an emphasis on qualitative superiority, diplomatic, economic and military support by major powers, importance of the principle of self-reliance and strategic autonomy, operationally offensive strategic culture among others.[30]

Israel’s prime ministers have left a lasting imprint on the country’s national security thinking. For instance, the ‘Ben-Gurion doctrine’ deeply impacted Israel’s strategic thinking until the 1980s. This doctrine was an outgrowth of the strategic environment that Israel faced in its early years.[31] Both as the Prime Minister and Minister of Defence, David Ben-Gurion authored a wide range of documents, through which he shared his national security vision.[32] Although not a codified concept, the Ben-Gurion doctrine encapsulates a combination of defence and offence and embodies the three principles of deterrence, early warning and offensive power.

Similarly, in the early 1980s, during the premiership of Menachem Begin, Israel formulated the ‘Begin Doctrine’ that sought to prevent countries hostile to Tel-Aviv from developing nuclear military capability.[33] The doctrine was put to motion when Israel, in an act of “anticipatory self-defence”, destroyed Iraq’s Osirak nuclear reactor in 1981. This was reaffirmed in 2007 against Syria’s suspected nuclear reactor.[34] Similarly, Naftali Bennett, who had a brief stint as Israel’s Prime Minister, encapsulated his approach towards Iran by propounding the “octopus doctrine”. Under the doctrine, Iran is seen as causing regional tensions, particularly along Israel’s borders, through its proxies, Hezbollah, Hamas and Islamic Jihad.

On Iran’s nuclear question, Prime Minister Netanyahu has shown no hesitation in sharing his scepticism about the nature of the Islamic Republic’s nuclear programme. In his autobiography, Netanyahu expresses his long-standing concern, revealing that he considered launching strikes on Iranian nuclear facilities as early as 2010.[35] However, he ultimately abandoned the plan due to opposition from the heads of the security services. He argued that

The mere fact that we were willing to risk retaliation for an attack would communicate to the Iranian regime how dangerous it would be to continue threatening us with nuclear weapons.[36]

Netanyahu also sought US support, but failed to convince successive administrations predisposed to reach a diplomatic solution. Netanyahu was determined to establish a clear “red line” on the Iranian nuclear programme, which he also visually expressed at the UNGA.[37] He vociferously opposed the JCPOA, as he perceived that the agreement failed to cover other elements, including ballistic missiles.[38] Even after the JCPOA agreement, Netanyahu continued to see the Iranian nuclear programme as an existential threat to Israel.

To further back his claim and Israel’s concerns, in 2018, Netanyahu publicly showcased a vast archive of documents, which he claimed were exfiltrated from Iran in an intelligence operation.[39] In his presentation at the Defense Ministry headquarters, he showed files, CDs and other documents linking them to Iran’s intention to develop nuclear weapons.

Successive Israeli leaders have consistently expressed deep distrust towards Iran’s nuclear programme. Frustrated by the international community’s failure to grasp its concerns fully, Israel resorted to alternative means to halt or sabotage Iran’s nuclear progress. To achieve its goals, albeit partially, Israel began deploying its attrition strategy to deter its enemies, particularly Iran. The MABAM[40] strategy, also known as “campaign between the campaigns”, was designed to “maintain and strengthen Israel’s deterrence between the major campaigns”, to dissuade its adversaries from targeting Israel.[41] This operational doctrine was formulated in response to growing Iranian entrenchment along Israel’s borders.

Militarily, MABAM entails the use of various types of force that resist growing threats to Israel’s security. Over the years, MABAM strategy has seen literal manifestation in Israeli operations, including efforts to intercept missile shipments from Iran to its regional proxies, particularly those along the Israeli border. Besides military campaigns, Israel’s attrition strategy also includes cyber operations, espionage campaigns and targeting individuals, aimed at thwarting threats to Israel emanating from Iran.[42] Although widely attributed to Israel, these operations are not publicly acknowledged by Israeli policymakers, who often refrain from commenting on such campaigns.

The campaign between wars also befits Israel’s strategy to diminish the enemy’s capabilities in preparation for the next war.[43] It also allowed Israel to disrupt Iranian advances continuously without triggering a major regional war. Deniability and ambiguity in these operations helped Israel avoid significant diplomatic backlash from international allies and partners. Furthermore, the shortlived intermittent campaigns place minimal strain on Israel’s economy, making them a key component of a broader strategy aimed at limiting the duration of combat.

It would be fair to say that while the current Israeli strikes against Iran reflect elements of the Begin doctrine, they also represent the cumulative strategies of successive Israeli governments, shaped by fundamental national security principles and their longstanding perception of the Iranian nuclear programme. Israel’s threat perception regarding Iran’s nuclear programme has also to be seen in the context of the 7 October 2023 attack against Israel. The surprise and unprecedented attack on Israel’s territory has led the IDF to pursue a multi-pronged strategy to tackle challenges on multiple fronts.

From Strategy to Operations

Over the last decade and more, Israel has carried out numerous kinetic and non-kinetic operations to thwart Iran’s regional entrenchment, alongside its nuclear and ballistic missile programme. A range of measures, including targeted assassination of military generals and scientists, believed to be closely associated with Iran’s nuclear and ballistic missile programme, cyber-espionage, and other forms of sabotage operations, were carried out by unidentified actors. While Israel has neither confirmed nor denied involvement, multiple assessments and reports widely attribute these actions to Israeli intelligence and defence agencies.

The first known non-kinetic operation against Iran’s nuclear facilities was the Stuxnet computer virus, allegedly jointly developed by Israel and the US.[45] Around 1,000 centrifuges at Natanz were rendered non-functional by the “first” cyberweapon.[46] In recent years, the focus of these operations has increasingly shifted towards targeting Iran’s ballistic missile and drone programmes. Multiple reports have surfaced detailing incidents ranging from drone strikes to various sabotage operations targeting Iran’s advanced weapons production facilities.[47]

Conclusion

Although the 12-day Israel–Iran conflict has ended in a ceasefire, the prospects for lasting peace remain minimal. The fragile peace depends on both sides abandoning their hardline stances. Iran’s nuclear programme which is seen by Israel as an existential threat is driven by Tehran’s own strategic calculations. Iran’s regional entrenchment through its proxies, particularly along Israel’s border, has only fuelled tensions. Similarly, Israel’s firm insistence on preventing Iran from attaining nuclear weapons, despite Tehran’s repeated denials, furthur complicates the matter. US strikes on Iranian nuclear facilities have further compicated the regional situation. Despite US and Israeli strikes on Iranian nuclear sites, most estimates note that the Iranian nuclear capabilites have remained largely intact. While the future of Iranian nuclear programme remains uncertain in the absence of IAEA’s oversight, Iran can use the threat of nuclear breakout as a leverage in two critical ways—negotiate a nuclear deal with the US or deter future military aggression against its territory.

Views expressed are of the author and do not necessarily reflect the views of the Manohar Parrikar IDSA or of the Government of India.

[1] Emanuel Fabian, “‘The Stars Aligned’: Why Israel Set Out for a War Against Iran, and What It Achieved”, The Times of Israel, 27 June 2025.

[2] Ibid.; “Operation Rising Lion: War Dashboard”, INSS, 24 June 2025.

[3] Emanuel Fabian, “‘The Stars Aligned’: Why Israel Set Out for a War Against Iran, and What It Achieved”, no. 1; Gram Slattery, Alexander Cornwell and Parisa Hafezi, “US Strikes Failed to Destroy Iran’s Nuclear Sites, Intelligence Report Says”, Reuters, 25 June 2025.

[4] “Israel Struck Heart of Iran’s Nuclear Enrichment Programme: Netanyahu”, India Today, 13 June 2025.

[5] Emanuel Fabian, “‘The Stars Aligned’: Why Israel Set Out for a War Against Iran, and What It Achieved”, no. 1.

[6] Emanuel Fabian, “Inspired by Brutal TV Scene, First Strikes on Iran Said Code-named ‘Red Wedding’”, The Times of Israel, 18 June 2025; “Operation Narnia: Iran’s Nuclear Scientists Reportedly Killed Simultaneously Using Special Weapon”, The Times of Israel, 20 June 2025.

[7] Andrew Mills, Parisa Hafezi and Alexander Cornwell, “Iran Fires Missiles at US Base in Qatar, Trump Calls for Peace”, Reuters, 24 June 2025.

[8] “Iran’s supreme leader makes first public appearance since Iran-Israel war started”, NPR, 6 July 2025; Amy Spiro, “These are the 28 Victims Killed in Iranian Missile Attacks During the 12-day Conflict”, The Times of Israel, 29 June 2025.

[9] G. Bahgat,  “Nuclear Proliferation: The Islamic Republic of Iran”, Iranian Studies, Vol. 39, No. 3, 2006, pp. 307–327.

[10] Atomic Energy Organisation of Iran.

[11] Alireza Nader, “Iran and a Nuclear-Weapon-Free-Middle-East”, Arms Control Association, 2011.

[12] “Nuclear Weapons and the Moral Compass: Islamic Position on Nuclear Weapons”, Global Security Institute.

[13] “Bushehr Nuclear Power Plant”, Nuclear Threat Initiative.

[14] Etel Solingen, “Nuclear Logics: Contrasting Paths in East Asia and the Middle East”, Princeton University Press, 2007, p. 165.

[15] “Implementation of the NPT Safeguards Agreement in the Islamic Republic of Iran”, GOV/2003/75, International Atomic Energy Agency, 2003. .

[16] “Implementation of the NPT Safeguards Agreement in the Islamic Republic of Iran Resolution adopted by the Board on 18 June 2004”, GOV/2004/49, International Atomic Energy Agency, 2004.

[17] United States, United Kingdom, France, China and Russia + Germany.

[18] “Expresses Concern at the Intentions of Iran’s Nuclear Programme and Demands that Iran Halt its Uranium Enrichment Programme”, S/RES/1696 (2006), United Nations Security Council, 2006.

[19] “Resolution 1929 (2010)”, S/RES/1929 (2010), United States Security Council, 2010.

[20] “At UN General Debate, Israeli Leader Calls for ‘Red Line’ for Action on Iran’s Nuclear Plans”, United Nations, 27 September 2012.

[21] Peter Beaumont, “Netanyahu Denounced Iran Nuclear Deal But Faces Criticism Within Israel”, The Guardian, 14 July 2015.

[22] “President Donald J. Trump is Ending United States Participation in an Unprecedented Iran Deal”, The White House, 8 May 2018.

[23] Marissa Newman, “Netanyahu: Israel ‘Fully Supports’ Trump’s Bold ‘Pullout’ from Iran Deal”, The Times of Israel, 2018.

[24] Robert E. Kelley, “Why is Iran Producing 60 percent Enriched Uranium?”, Stockholm International Peace Research Institute, 2021.

[25] “Update on Developments in Iran (5)”, International Atomic Energy Agency, 2025.

[26] “Missiles of Iran”, Missile Defense Project, Centre for Strategic and International Studies, 2021.

[27] Charles D. (Chuck) Freilich, “Israel’s National Security Strategy”, in P.R. Kumaraswamy (ed.), The Palgrave International Handbook of Israel.

[28] Amir Vahdat and Jon Gambrell, “Iran Leader Says Israel a ‘Cancerous Tumor’ to be Destroyed”, AP News, 22 May 2020.

[29] Erik Skare, “Iran, Hamas, and Islamic Jihad: A Marriage of Convenience, European Council on Foreign Relations”, European Council on Foreign Relations, 18 December 2023.

[30] Charles D. (Chuck) Freilich, “Israel’s National Security Strategy”, no. 27.

[31] Charled D. Freilich, Israeli National Security: A New Strategy For An Era of Change, Oxford University Press, 2018.

[32] Kim Bar, “Aspects of the Formation of Israel’s National Security Doctrine”, Dado Center for Interdisciplinary Military Studies, October 2024.

[33] Amos Yadlin, “The Begin Doctrine: The Lessons of Osirak and Deir ez-Zor”, INSS, 21 March 2018.

[34] “To Prevent a Nuclear Iran, It is Time to Bring Back the Begin Doctrine”, The Jerusalem Post, 18 April 2025.

[35] Benjamin Netanyahu, Bibi: My Story, Threshold Editions, 2022.

[36] Ibid., p. 479.

[37] Jeffrey Heller, “Netanyahu Draws ‘Red Line’ on Iran’s Nuclear Programme”, Reuters, 28 September 2012.

[38] Benjamin Netanyahu, Bibi: My Story, no. 35, p.524

[39] David Horovitz, “‘Iran lied’: Netanyahu Drops a Mossad Bombshell on the Iranian Nuclear Deal”, The Times of Israel, 30 April 2018.

[40] Denotes campaign between the wars known in Hebrew as m’aracha bein ha-milchamot or, more succintly by the acronym mabam.

[41] Charled D. Freilich, Israeli National Security: A New Strategy For An Era of Change, no., p. 225.

[42]  Anna Ahronheim, “MABAM: Israel’s Strategy to Chase Iran, Proxies Out of Syria”, The Jerusalem Post, 7 October 2022.

[43] Eran Ortal, “The Fly on the Elephant’s Back: The Campaign between Wars in Israel’s Security Doctrine”, INSS, April 2021.

[44] Jacob Nagel and Jonathan Schanzer, “From Ben-Gurion to Netanyahu: The Evolution of Israel’s National Security Strategy”, Foundation for Defense of Democracies (FDD), 13 May 2019.

[45] “Timeline: Israeli Attacks on Iran”, The Iran Primar, 31 July 2024.

[46] David Kushner, “The Real Story of Stuxnet: How Kaspersky Lab Tracked Down the Malware that Stymied Iran’s Nuclear-fuel Enrichment Programme”, IEEE Spectrum, 20 June 2025.

[47] “Timeline: Israeli Attacks on Iran”, no. 45.