Introduction

When the war between Israel and Iran finally draws to a close, a new uncertainty will loom: the future of Iran’s nuclear weapons programme. As smoke clears from damaged nuclear sites and diplomats eye a possible peace settlement, observers will ask whether Tehran will truly halt its nuclear ambitions under a renewed deal – or simply hide them better. The question is not merely academic; it cuts to the core of Middle East security and global non-proliferation efforts. Iran’s leaders insist their nuclear programme is peaceful, yet years of cat-and-mouse with inspectors and secret development activities tell a more complicated story. In the aftermath of war, will a new nuclear agreement genuinely curb Iran’s weapons programme, or just drive it further underground? This analysis examines Iran’s track record on nuclear compliance, the conflicting claims about its weapons potential, and the scenarios for what comes next in a post-war landscape.

Iran’s Nuclear Agreements: A History of Compliance and Evasion

Iran’s engagement with nuclear accords has been marked by both adherence and deception. On paper, Iran is a party to the Nuclear Non-Proliferation Treaty (NPT) and has repeatedly stated it does not seek atomic bombs. In practice, however, its past actions reveal a checkered compliance history. In the early 2000s, the International Atomic Energy Agency (IAEA) discovered that Iran had concealed significant nuclear work – including uranium enrichment facilities at Natanz and a heavy water reactor at Arak – in violation of its safeguards obligations. Subsequent investigations indicated Iran had a coordinated nuclear weapons programme (the secret Amad Plan) until 2003, aimed at designing at least five warheads[1]. Under international pressure and fear of military strikes, Tehran appeared to halt the weapons programme in 2003, but evidence suggests it only downsized and carried parts of it into deeper secrecy[2]. In fact, intelligence seized from Iran’s own archives in 2018 revealed that by 2003 Iranian scientists were preparing for a “cold test” of a nuclear explosive – the final step before building a prototype – and had developed a workable bomb design about the size of a car tire[3]. This indicates that even as Iran publicly denied seeking nukes, it was far closer to a weapons capability than previously known.

 The 2015 Joint Comprehensive Plan of Action (JCPOA) temporarily put the brakes on Iran’s programme. Under this landmark nuclear deal, Iran shipped out large stockpiles of enriched uranium, capped enrichment at a low 3.67% purity, and submitted to rigorous IAEA inspections. By all public accounts, Iran initially complied with the JCPOA’s strict limits. The IAEA confirmed through quarterly reports that Tehran stayed within the agreed caps on enrichment level, uranium stockpile size, and centrifuge numbers[4]. Even after the United States unilaterally withdrew from the accord in 2018 (citing that Iran was already breaching the agreement), Iran was said to have remained within key restrictions for some time as European powers tried to salvage the deal[5]. However, when promised economic relief failed to materialize, Iran began openly breaching the deal in 2019. Over the next few years, Iran systematically violated JCPOA constraints: exceeding the 300 kg limit on low-enriched uranium, enriching above the 3.67% level (first to 4.5%, then 20%, and eventually 60% purity), and deploying advanced centrifuges beyond the allowed types and numbers. Each step was calibrated to pressure the West, but cumulatively it eroded trust that Iran would honour nuclear agreements long-term.

 By 2023–2024, Iran’s nuclear programme not only bounced back but surpassed its pre-deal status. Tehran amassed a stockpile of uranium enriched up to 60% U-235 – a level with virtually no civilian use, approaching weapons-grade quality[6]. The IAEA has voiced alarm at this trajectory, bluntly noting that Iran is the only non-nuclear-weapon state producing highly enriched uranium at such scale, a situation it called “of serious concern”[7]. Compounding matters, Iran dramatically reduced monitoring cooperation. It disconnected IAEA surveillance cameras, ceased adhering to the Additional Protocol’s snap inspections, and in 2024 even expelled several experienced IAEA inspectors from its nuclear sites[8]. These moves left inspectors with greatly impaired oversight. As of May 2025, the IAEA reported Iran’s total enriched uranium stockpile had swelled to over 9,000 kilograms, including more than 400 kg of 60%-enriched material – enough, if further refined, for multiple bombs[9]. Such facts stand in stark contrast to Iran’s statements of peaceful intent.

Conflicting Narratives: Peaceful Programme or Bomb Ambitions?

Tehran has long been walking a fine line between its public stance and the suspicions of the international community. Iranian officials consistently assert that nuclear weapons have no place in Iran’s defence doctrine. Supreme Leader Ayatollah Ali Khamenei even issued a fatwa (religious edict) against the production or use of nuclear arms. As recently as April 2024, Iranian representatives reiterated that “nuclear weapons have no place in our doctrine,” insisting Iran’s nuclear pursuits are solely for energy and research[10]. This narrative portrays Iran as a principled actor abiding by its commitments and suffering unjust scepticism.

 Yet global authorities and experts offer a contradictory view, backed by years of evidence. The IAEA’s own investigations concluded that Iran did undertake weaponization work prior to 2004 – something Iran vehemently denied at the time. Western intelligence agencies, while differing in tone, largely concur that Iran wants the option to build nuclear weapons even if it hasn’t assembled one yet. U.S. and European intelligence assessments up to mid-2025 continued to say that Iran had not actually constructed a nuclear warhead or made the political decision to do so[11]. However, they also describe Iran as a threshold nuclear state – one technical step away from weapons capability. Israeli officials, facing a country that has vowed to destroy the Jewish state, tend to be more sceptical of Iran’s intentions. Israel’s government openly warns that Iran’s accelerating enrichment and ballistic missile work point to an undisclosed weapons effort, and Israeli intelligence has hinted that Iran may be conducting secret weapon-related experiments beyond the eyes of inspectors.

 These competing narratives are reflected in a flurry of contradictory statements over the years. The IAEA, for its part, has tried to stick to facts on the ground. In June 2025, just days before the war erupted, the Agency’s Board of Governors formally censured Iran for failing to fully cooperate with inspections – the first such rebuke in two decades. Rather than assuage concerns, Tehran reacted defiantly by announcing plans to open a third uranium enrichment site and install more advanced centrifuges, effectively accelerating its programme[12]. At the same time, independent analysts have pointed to multiple known violations and covert activities that suggest Iran’s weapons ambitions never disappeared. For example, Iran secretly built the Fordow enrichment plant under a mountain years ago and only admitted its existence when exposed in 2009. More recently, Iranian nuclear scientists embarked on experiments with uranium metal – a material used in nuclear bomb cores – despite such work being banned under the JCPOA. IAEA inspectors have also found unexplained traces of man-made uranium at undeclared locations in Iran, indicating possible secret nuclear material that Iran hasn’t accounted for. Each discovery feeds the view that Iran’s “peaceful” programme may be a facade masking clandestine weapons-related work.

 Perhaps most striking are suggestions that Iran may already have a nuclear weapon – or at least the pieces of one. Thus far, no conclusive public evidence shows Iran possesses an operational nuclear warhead. Both U.S. and Israeli officials maintain that as of now Iran has not built a functioning bomb[13]. Nonetheless, the very fact that this question is asked underscores the deep uncertainty. Over the years, rumours have surfaced about Iran obtaining nuclear hardware from abroad or assembling a crude device in secret. In fact, the CIA warned back in 2001 that it “could not rule out the possibility” that Iran might have acquired fissile material on the black market and perhaps even a weapon capability[14]. Some Iranian figures have hinted at undeclared advances – in 2022, a former Iranian official startled observers by musing that Iran might already have a nuclear weapon, though offering no proof. Analysts at the Institute for Science and International Security note that Iran had achieved the know-how by 2003 to design a workable implosion device and was on the cusp of a prototype test before the project was paused[15]. It’s conceivable that Iran preserved those weapon blueprints (indeed, Israel’s 2018 archive seizure showed they did) and could have built an untested “cold” prototype in the ensuing years. All of this remains speculative – but the mere existence of such speculation highlights how little transparency there is about the true endgame of Iran’s nuclear endeavours[16]. The world might not know immediately if Tehran crosses the nuclear threshold, especially after Iran’s curtailment of monitoring[17].

Covert Activities and Known Violations

Iran’s pattern of behaviour in the nuclear realm often involves playing for time and pushing boundaries in secret. History shows that when faced with intense scrutiny or pressure, Tehran tends to hide or harden its nuclear assets rather than eliminate them. A prime example is what happened after 2003: Iran’s leaders ordered a downsizing of the overt weapons programme to avoid international backlash, but they carefully preserved the core expertise and shelved projects for potential reactivation[18]. Many activities simply migrated to academic or military institutions under the radar. This strategy of burying the programme deeper paid off – Iran managed to continue enrichment and research in quieter ways until it eventually had tens of thousands of centrifuges operating. In the late 2000s, Iran fortified key facilities like Natanz with bunkers and built new secret sites such as Fordow inside a mountain, literally burying critical parts of its programme to protect them from airstrikes. Every time one path was blocked by sanctions or sabotage, Iranian nuclear scientists found a workaround or created a fallback clandestine project.

 Even under the JCPOA, when Iran’s nuclear work was largely in the open, there were hints of stealth. Israeli intelligence famously infiltrated a Tehran warehouse in 2018 and recovered a “Nuclear Archive” – a vast collection of files detailing Iran’s weapons plans and research. The archive’s existence was itself a violation of Iran’s commitments (since keeping design information for nuclear weapons contradicts pledges of peaceful intent)[19]. That Iran held onto these files strongly suggests it intended to resume bomb work at a time of its choosing. Additionally, as soon as the JCPOA’s enforcement faltered, Iran resumed proscribed activities at remarkable speed – installing advanced IR-6 centrifuges, enriching uranium to 60%, and producing uranium metal, none of which have a credible civilian justification in the quantities Iran pursued[20]. In short, Iran has often violated agreements or exploited their loopholes while denying any wrongdoing. This dual-track approach (public compliance, private non-compliance) means any new promises by Tehran will be met with a great deal of scepticism.

 The recent Israel-Iran war itself revealed the extent of Iran’s covert build-up. Israel’s strikes targeted not only known enrichment halls but also shadowy installations that had been off-limits to inspectors. Reports indicate that a new underground facility near Natanz – so deep that it may be beyond the reach of conventional bunker-busting bombs – was under construction to house centrifuges. Such a site, once operational, could allow Iran to enrich uranium out of sight and reach, effectively immunizing its weapons programme from future military intervention. This underscores a troubling possibility: Iran might agree to a nuclear deal on paper while simultaneously moving the most sensitive work to undeclared or impregnable locations. The IAEA has already warned that its knowledge of Iran’s activities is diminishing due to lack of access. Without robust verification, Iran could cheat on a deal by continuing weapons-related work covertly, as North Korea did in the 1990s. All these known violations and secret projects form the backdrop against which any post-war nuclear deal will be judged.

Post-War Scenarios: Halt, Hide, or Speed Up?

With a tentative peace settlement now on the horizon, the big question is how Iran will proceed on the nuclear front. Several distinct scenarios could unfold, and each carries its own implications for regional security:

 1. Genuine Halt Under a New Deal: In the most optimistic scenario, Iran might agree to fully halt its weapons programme in exchange for sanctions relief and security guarantees as part of the peace deal. War has been punishing for Iran – key nuclear facilities are damaged, the economy is strained, and the regime may calculate that a period of true restraint is necessary for recovery. A new nuclear agreement, perhaps a revived JCPOA or a strengthened version of it, could be the vehicle. If Iran’s regime feels confident it will remain in power (thanks to the peace settlement) and fears further military strikes, it might conclude that adhering to strict limits is its best move, at least temporarily. This would mean Iran once again shipping out enriched uranium, dismantling excess centrifuges, and allowing intrusive inspections anywhere suspected of nuclear work. The international community would undoubtedly push for tougher terms than the 2015 deal – for example, immediate access for IAEA to suspect military sites, longer-lasting restrictions (no automatic sunset clauses), and constraints on missiles capable of carrying nukes. Proponents of diplomacy will argue that a new deal could meaningfully delay Iran’s nuclear progress and prevent a regional arms race. However, even in this best-case scenario, scepticism will linger. Iran would need to prove over time that this halt is genuine, and not just a pause to regroup. Any small violation or evasion would be seized upon as a sign that Iran is burying the programme out of sight. The success of this path hinges on unprecedented transparency from Tehran – something it has resisted in the past.

 2. Burying the Programme Deeper (Covert Continuation): A more cynical scenario is that Iran agrees to a deal and outwardly curtails parts of its nuclear programme, but covertly continues developing the know-how and components for weapons. In this scenario, a nuclear deal might halt the visible activities (like large-scale enrichment) while the regime furthers its weapons ambitions underground. Iran has a playbook for this: after 2003, it preserved its nuclear weapons intellectual capital and hid sensitive research within defence agencies[21]. If a new agreement is signed, Iran could comply with inspector visits at declared sites even as it shifts any banned work to clandestine facilities or shell companies. For example, weapon design work could be pursued by a small team under the guise of conventional military R&D, or enrichment could be secretly carried out on a much smaller scale at an undeclared pilot plant. The risk is that the world might be lulled into a false sense of security while Iran’s nuclear programme is simply driven deeper into the shadows. Multiple analysts warn of this outcome. The Institute for Science and International Security cautions that reimplementing a JCPOA-like deal without much tougher verification would be “unstable and dangerous,” likely leading to more covert activity and a worsened security situation[22]. In essence, a deal might buy time but also provide cover under which Iran’s nuclear progress continues out of sight. To counter this, negotiators would need to insist on far-reaching inspection rights and real-time monitoring of the entire supply chain of Iran’s nuclear-related materials. Even then, confidence in Iranian compliance would be low. This scenario – halting the programme publicly while burying it deeper privately – would fulfil the fears behind the question posed: that a nuclear deal might not stop Iran’s weapons drive at all, only conceal it better.

 3. Redoubling Efforts and Speeding Up: The third scenario is the most alarming: Iran, embittered by the war and distrustful of any promises, could decide to accelerate its push for a nuclear deterrent as quickly as possible. Having just experienced devastating Israeli airstrikes, Iranian hardliners may be convinced that only an actual nuclear weapon can guarantee their nation’s security against future attacks. “Iran will redouble the effort to develop their nuclear weapons programme if they are not stopped now. They just discovered they are incapable of defending against Israel,” warned the Director of the DEFCON Warning System on June 14, 2025[23]. Indeed, the war’s outcome – with Iran’s conventional defences proving no match for Israel’s high-tech military – likely reinforced the argument of those in Tehran who always saw nuclear arms as the great equalizer. If the current regime remains in power post-war, it may view a bomb as the only insurance against regime change or invasion. Iran might rebuild and fortify its nuclear sites with haste, install hundreds of new centrifuges in hard-to-bomb locations, and potentially carry out a nuclear test in the not-too-distant future to announce itself as a nuclear-armed state. Such a course would be extremely provocative – almost certainly triggering a crisis with the West and possibly pre-emptive military action by Israel or the United States. Yet it cannot be ruled out. The logic of deterrence that other nations have followed might appeal to Iranian strategists: North Korea, after all, obtained nuclear weapons and has largely deterred direct attack since. If Iran’s leaders conclude that the world failed to stop them during this war and that future wars are inevitable, they may choose to sprint for a deliverable nuclear weapon while they still can. This path would dramatically raise the risks of a renewed conflict, this time possibly nuclear.

 Of course, reality might not fit neatly into any one of these scenarios – Iran’s course could be a mix of public compliance and quiet hedging. It’s also possible that internal Iranian politics (such as a change in leadership or public sentiment after a costly war) could alter Tehran’s calculus in unexpected ways. For instance, a weakened regime might double down on nationalism and the prestige of a bomb, or alternatively a more moderate faction might gain influence seeing the ruinous cost of isolation. What is clear is that Iran’s post-war nuclear trajectory will not be linear or easily managed. Every path forward – halting, hiding, or speeding up – comes with high stakes and perilous uncertainties for the region and the world.

Conclusion

As Iran and Israel step back from the brink, the fate of Iran’s nuclear weapons programme hangs in the balance. A new diplomatic effort may emerge to contain Tehran’s atomic ambitions once more, but the trust deficit is enormous. Iran’s history of half-truths and evasions means any promise it makes will invite doubt, while the regime’s survival instinct (sharpened by war) gives it strong incentive to secretly seek a deterrent. A revived nuclear deal could temporarily freeze the most dangerous parts of Iran’s programme, yet sceptics worry this would simply lull the world into complacency as Iran conceals its work in underground bunkers. On the other hand, refusing a deal and pursuing all-out nuclear weapons development would court disaster, potentially inviting pre-emptive strikes that trigger another war – one that could go nuclear.

 For now, Iran remains officially non-nuclear, and there is a narrow window to reinforce that reality. The aftermath of war provides urgency: both the West and regional players will push hard to prevent Iran from rebuilding a path to the bomb. The onus will be on Tehran to choose a path of restraint or face isolation (or worse). Any new agreement must come with unprecedented transparency measures to ensure Iran isn’t simply burying a weapons programme out of sight. Likewise, the international community will need to stay united and firm that an Iranian nuclear weapon is unacceptable, while avoiding steps that could needlessly drive Iran towards the bomb out of fear. It is a delicate balance.

 In the end, whether a nuclear deal will halt Iran’s weapons programme or just bury it deeper will depend on the actions of the Iranian regime when it thinks the world is not watching. History provides ample reason for worry – but also one faint hope: that having seen the brink of destruction in war, Iran’s leaders may decide that nuclear restraint serves their survival better than nuclear brinkmanship. Only time (and vigilant verification) will tell which path Iran chooses in the shadow of war’s end.