The Twelve Day War between Israel and Iran may seem like a short burst of conflict that was contained in its scope, but might prove in the long term to be a fuse that was lit to the regional powder-keg. The US intervention that appears like having been almost an exit ramp might turn out to have made the region far more combustible than it was before the misadventure. The ceasefire is not a truce, and extremely unlikely to pave the road to peace from what it portends.

The US-Iran Nuclear Talks

From the time Trump made his way back to his second term at the White House, Tehran had been on pins-and-needles. The Islamic Republic of Iran had been flying kites about returning to the negotiation table soon after Masoud Pezeshkian became President in the summer of 2024, but was not particularly keen on settling the matter under Biden unless he was guaranteed a second term. After the Presidential elections were held, Tehran did not entertain much hope of a negotiated settlement. Hence when Trump offered talks, Tehran was not quite certain about what to make of it. The national security component of the Iranian establishment, represented predominantly by the hardliner-IRGC axis, was not keen on the talks at all. But the decimation of Hamas and Hizballah, general weakening of the Axis of Resistance across the extended neighbourhood in the face of Israeli offensive, and most importantly Israeli success in severely damaging Iranian air defences after the October 2024 strikes – all these had reduced the leverage of the hardliner position. This served to have the Supreme Leader to agree with the reformist-pragmatist components in Iranian politics to explore the possibility of direct negotiations with the USA – but apparently with the strict proviso that there would be no consideration for the Libyan model of renouncing nuclear capability. Foreign Minister Abbas Araghchi was sent with the defence of the consensual position that has characterized the Iranian establishment on the nuclear issue for the last three decades – that Iran develops nuclear weapons capability but remains a nuclear-threshold state, without actually building the bomb. This conformed to the stated position of Tehran since 2003, that Iran is not developing nuclear weapons.

By contrast, the Americans did not seem to have entered the nuclear talks with a clear position, except that President Trump, ‘the Great Dealmaker’, wanted a deal. When the JCPOA was concluded in 2015, Iran was believed to have been around a year away from breaking out as a de facto nuclear weapons power. After Trump pulled out of it in 2018, intelligence inputs suggested Iran started enriching uranium up to 60%, and the break-out time was believed to have reduced to either a few weeks or a few months. It would seem that the American ‘deep state’ sensed a last opportunity to return to negotiations over Iran’s nuclear programme, and was able to persuade Trump on the need for a deal. But Trump’s inability to trust the American ‘establishment’ had him entrust the negotiations to Steve Witkoff, a New York based lawyer specializing on property matters. Confronted with Abbas Araghchi, who was a key member of the team during the JCPOA, Witkoff seems to have proven out of his depth. Hence after the first two rounds in Doha and Rome, as Tehran became confident of being able to return to something like a JCPOA 2.0 arrangement, Trump came under pressure from the ‘establishment’ (and also possibly Israel) to say that not only could Iran not be allowed to make nuclear weapons, it would not even be allowed to enrich uranium for civilian purposes either – which, being an NPT signatory, was a right Tehran could not be denied under international law. Critics of JCPOA became vocal that Witkoff was essentially leading US back to a JCPOA-like deal, and even after five rounds of talks till early June, was yet to broach the issue of Iranian missile development programme.

By early June, proponents of a nuclear settlement on both sides were hopeful that Tehran would settle for returning to the right to enrich uranium up to 3.67% (as agreed under the JCPOA), and could be persuaded to give up the 400-odd kg of uranium enriched up to 60% (a short way from the critical marker of 90%) to some third power. Tehran even proposed pursuing its civilian nuclear power programme in a consortium with its Gulf Arab neighbours, and also proposed direct American participation in Iranian economy and even in nuclear research activities in days to come. Witkoff was hopeful that an IAEA verification regime more intrusive than the JCPOA would ensure that the allegedly-clandestine dimension of Tehran’s nuclear programme would be successfully killed. However, Trump appeared to begin to yield to hardline Republican pressure to have Iran abandon its right to uranium enrichment altogether, which neither Araghchi would, nor the Iranian hardliners could allow him to, accept.

This was the point where the talks were poised on 12th June 2025, when the IAEA Governing Body declared Tehran to be in breach of its NPT commitments for the first time in 20 years, failing to account for some traces of uranium enriched up to 83.7%. The day after Israel began its air-strikes on Iranian nuclear and military targets.

The Israel Factor

Even though Iran has routinely denied all allegations of developing a nuclear weapons programme, and the international community has never proved these allegations beyond a reasonable doubt, Israel has consistently and forcefully levelled those charges right from 2003. Widely believed to be a nuclear weapons power itself (which it neither affirms nor denies), Israel has been in the forefront of efforts to prevent Iran from developing nuclear weapons capability, let alone produce nuclear weapons. Israel has been pretty consistent in its opposition to pursuit of nuclear weapons in its neighbourhood, having resorted to the military option against Iraq (1981) and Syria (2007) before this. Given Iran’s higher military profile, Tel Aviv refrained from the military option, but has in the past tried to expose the Iranian nuclear programme by actually seizing Iran’s entire nuclear archives through espionage operations (2018), and tried to slow it down through cyber-attacks and then periodically assassinating high-profile Iranian nuclear scientists

Ever since the outrage of 7th October 2023, Israel appears to have resigned itself to the likelihood that neither a one-state nor a two-state solution could work with the Palestinian question. Hence, it seems to have decided on applying overwhelming force in Gaza. Simultaneous attacks from Hizballah of Lebanon and from the Houthis in Yemen in solidarity with Hamas made Israel extend the arc of conflict by going beyond its own boundaries pursuing the militias deep into their own territory to hunt them down. Within a span of a year, Israel not only crippled Hamas but also effectively crippled Hizballah by decapitating virtually its entire leadership, including Hassan Nasrallah. In a shadow war in Syria and Iraq in the last decade, Israel had been targeting Iranian IRGC operatives in Syria as well to undermine its support for Hizballah and to push back Iran’s expanding zone of influence. In 2024 it raised its policy of targeted killings a notch higher by carrying out assassinations of IRGC functionaries in Damascus, the heart of Assad’s Syria (Iran’s only regional ally), and then of the Hamas leader Ismail Haniyyeh in the heart of Tehran.

Although Tehran seems to have been determined to steer clear of conflict till then, it felt compelled to retaliate against strikes on its consular building in Damascus and in the heart of its capital. This resulted in two tit-for-tat strikes by Iran and Israel against each other – April and October 2024. While these were intended as acts of measured escalation by both sides without a desire for larger conflict, they did constitute the first attack on Israel by another country since 1973 and on Iran since 1988. Hence the assumptions of military deterrence that informed defence policies of both these countries were left shaken. In October, Iran’s success in landing at least twenty missiles past Israeli defence shield shredded Israel’s myth of military invincibility; in return, Israel’s retaliation created a major dent in Iran’s air defence capabilities.

It is reasonable to presume both sides went back to the drawing board with their defence policies after October 2024. When Trump made it back to White House, Netanyahu seems to have immediately begun pressing him to tighten the screws on Iran’s nuclear programme and for a military solution, including (it would now seem) for regime change. Trump settled instead for nuclear talks, dangling the prospects of an Israeli attack on Tehran’s nuclear installations as a way of persuading Tehran back for talks.

However, after five rounds of talks, Tel Aviv was not happy with the emerging outcome, because the Israeli establishment felt Araghchi was running the rings around Witkoff, and feared Tehran would retain its nuclear weapons programme and would even be able to build nuclear weapons within a very short time – arguably three weeks to enrich uranium to 90%, and at most another few months to develop delivery capability. This was unacceptable to Israel even if Washington settled for it. Further, Tel Aviv was acutely aware that Iranian air-defence, down since October 2024, would not necessarily remain down for long. Thus, Israel decided to move in while it could when the IAEA flagged Iran’s non-compliance with its NPT commitments, in order to militarily push back Tehran’s nuclear ambitions since negotiations didn’t appear like achieving that any more.

A Lion Playing with a Hammer

In the 12 days of conflict that followed, a number of things became clear. As anticipated, Israeli air force was able to establish dominance over Iranian airspace with effortless ease, and went about carrying out airstrikes against some of the facilities associated with the Iranian nuclear programme (Tehran, Natanz, Esfahan, Arak) and military installations and capabilities (such as missile launchers). Additionally, Israel went about hitting targets associated with the IRGC, including a number of their top brass including the IRGC Commander, Hossein Salami. Since most of Iranian nuclear facilities and IRGC and military targets were either close to, or in, civilian populated areas, the collateral damages were quite high (over 500 in 12 days).

On the other hand, while Iran was alarmingly incapable of protecting its own airspace, and while its retaliatory strikes against Israel did not appear to have inflicted comparable damages to either Israel’s military capabilities or civilian infrastructure (with less than 30 lives lost), the very fact that Iranian missiles managed to penetrate the three layered (Arrow, David’s Sling, Iron-Dome) anti-missile defence systems (with US support) was quite disturbing for the Israeli establishment. Coming as they did without careful telegraphing (as in April and October 2024), clearly Iranian ballistic missiles are able to overwhelm Israeli missile defence systems if the salvos are timed right. Within a week of the conflict Israeli Defence Forces were left anticipating that they might run out of their interceptor missiles before Iran ran out of its LRBM and IRBMs.

It would seem that given what was turning out to be a strategic stymie, Bibi Netanyahu solicited American intervention – particularly to inflict crippling damage on installations like Fordow (which were known to be beyond the range of all munitions worldwide except American bunker-busters dropped from B-2 bombers). It would also seem that a segment of the Pentagon (and presumably some Republican neo-cons) suggested to Trump ‘one-and-done’ air and missile strikes against the more critical Iranian nuclear installations, which could possibly be carried out within that small window of opportunity provided by complete Israeli domination of the Iranian air-space. Hence after the initial distancing from Israeli military ventures against Iran, Trump went ahead to embrace these and briefly even join it – hoping that the strikes against Fordow, Esfahan and Natanz would cripple the Iranian nuclear programme, without causing wider escalation. Thus, when Tehran decided to limit its retaliation to missile strikes against American airbase in al-Udeid, Qatar (after carefully telegraphing it to avoid any serious damage to either Qatar or the USA), Trump offered both Tehran and Tel Aviv an exit ramp, which both seem to have accepted quite readily (mindful of their respective vulnerabilities).

Significance of the Military Escapade

From the finesse with which Israel bumped off IRGC functionaries and other regime targets, it becomes very clear that IDF had penetrated deep inside the Iranian establishment, and had plans ready for something like this – at least since October 2024, if not earlier. But chatter suggests that IDF was divided on launching Operation Rising Lion at this time, coming as it did in the wake of Israeli entanglement in Gaza and elsewhere in the neighbourhood (i.e. Syria and Lebanon). The decision to go in was, in the main, political, backed up by the military intelligence input that Iran had best be attacked before it could repair its air defence systems. It is unlikely that Tel Aviv bargained on regime change, although (as Bibi repeatedly said) they considered the possibility as both desirable and probable. It is equally unlikely that Israel bargained on either an easy victory, or a long-drawn conflict. It is very likely that Israel moved with the highly ambitious goal of merely setting back Iranian nuclear weapons programme by a year (or a few years at best) – not destroying the Iranian nuclear programme altogether. It also wanted to, if possible, to drag the US into the conflict, precisely so that the conflict became neither long drawn, nor broadened beyond a point – because Tehran was unlikely to have risked the stability of its own regime.

Did Trump get played by Bibi? That would not seem to have been the case. A section of the American establishment had always been critical of the limitations of the JCPOA, but there indeed seems to have been a broad consensus that Iran’s nuclear ambitions were not susceptible to a military solution. The JCPOA was possibly the only viable approach to desist Iran from pursuing nuclear weapons, by delaying it long enough to rehabilitate Iran in the global economy. It was hoped that thereafter Tehran would be wary of being hit by crippling sanctions regime yet again by going nuclear. Having pulled the plug on it, Trump had in effect pressed Tehran in the opposite direction. For America to stage a return to the JCPOA paradigm, Tehran had to be re-engaged with the same carrot. With the opportunity provided by Israel’s domination of the Iranian fire-space, USA seems to have thought of pushing Iranian nuclear programme back to a point it would once again be regressed to a projected break-out time of a year or more, before returning to the negotiation table for a deal that would be as favourable as the JCPOA or more. This just might turn out to be a miscalculation.

As to Iran, if it had any strategic objectives in the last six months, it would have been to steer clear of any conflict, for fears of regime security – not so much from external threats as from the possibility of domestic upheaval during a prolonged conflict that could have made economic hardship of the last 15 years altogether unbearable. Clearly, Iran failed to achieve that objective. However, the Islamic Republic attained its ultimate objective of thwarting off regime change. It is now clear that Iranian establishment is very severely compromised by Israeli intelligence penetration. Tehran has already started the process of hunting out the moles – if it does not use this wake-up call seriously, and indulge in merely silencing voices of dissent, Iran would pay the price at a later date.

Far more importantly, Tehran is likely to have learnt a few other lessons that do not augur well for peace in the region. Apart from the assumptions about its military capacity being an effective deterrence (which has been shredded by the Israelis), Tehran also seemed to have assumed that while Israel might fight shadow wars on third country soil and assassinate nuclear scientists, it would not risk a short-to-long-term direct confrontation with Iran – that theory lies in tatters. Till this point, Iran actually had no real cause for conflict with Israel except for the tactical consideration of keeping the pot boiling in occupied Palestine, and arming the Hizballah on Israel’s northern border. This was to ensure that Israel remains on the edge and America remains tied down supporting Tel Aviv – every time US pressure on Iran increased in the past, Tehran opened a second front to distract the US. By degrading military capabilities of Hamas and Hizballah, Israel has robbed Iran of these two cat’s paws; the collapse of the Assad regime in Syria makes it almost impossible to rebuild and refurbish either of them. Thereafter, there was a good possibility that Tehran would have done little beyond licking its wounds for some time. However, by attacking Iran directly, and openly invoking anti-regime forces to dislodge the Islamic Republic, Tel Aviv has given Iran a casus belli for the first time. In the foreseeable future, Iran would probably be found concentrating on refurbishing its military hardware with a war against Israel in mind, more than anything else. The next Israel-Iran war would probably cause greater damage on both sides.

With respect to the United States, there have always been a large segment of the Iranian population, and a fairly sizeable segment of the Islamic Republic’s establishment, who have always desired close (or at least normal) ties with America. Reformists during the presidential tenures of Khatami, Rouhani and now Pezeshkian have been keen on mending fences with Washington, but were held back by hardliner’s suspicion of American hostility to the Islamic Republic. Even then, during the JCPOA and the latest round of nuclear talks, Tehran seems to have assumed that while it was engaged in negotiations with the USA, there is no risk of starting a conflict. Not only did Israel make short work of that theory, by participating in the attacks on Fordow, Natanz and Esfahan, the USA seems to have added to the shock. Here onwards, in the unlikely event of Tehran returning to talks with the USA in a hurry, it would come with far less faith in American interlocutors than had made the JCPOA possible.

Most crucially, by exposing Tehran’s military vulnerabilities before their combined overwhelming military might, Israel and USA may have reinforced the most persuasive argument for Iran persevering on the nuclear path. Given the existing sanctions regime, Iran’s defensive capabilities are unlikely to be ever brought up to scratch. With the Axis of Resistance also steering studiously clear of involving itself in Iran’s hour of trouble, their reliability to rally behind Iran would be limited by their own calculations. Hence, in absence of other viable alternatives of regime security, the arguments for Iran’s pursuit of the nuclear option are stronger than ever.

In this respect the crucial question is how viable is the nuclear option for Iran in the light of the Israeli and American nuclear strikes. American defence and intelligence assessments indicate that the success of the strikes on Natanz, Esfahan and Fordow have been exaggerated by President Trump. There is a possibility that Iran may have successfully removed the 400 kg of uranium enriched to near weapon’s grade (either in Iran itself, or to some third country); it may even be the case that the enriched uranium lies buried under the rubble somewhere – in both cases Iran can retrieve the stockpile once they have repaired/rebuilt their existing enrichment facilities (Natanz, Esfahan). Iran may have some other enrichment facilities that are not known about, and could even build new facilities deeper underground than even at Fordow the next time. All of this might take some months, and Iranian nuclear programme may have been slowed down by only that much time – no one seems to be entertaining the illusion that the Iranian nuclear threat has been put to an end.

Would Tehran Return to the Negotiation Table?

It is too early to conjecture what Tehran could do next. Much would depend on what happens next inside the body-politic of the Islamic Republic.

The Israeli assassination of targets high up in the IRGC or the Iranian establishment generally, was meant to have weakened the Islamic Republic, and opened it up to popular upheaval. While upheaval never came about, the assassinations may have stirred things up a bit. The successor of Hossein Salami as the Head of the IRGC, Mohammad Pakpour, along with a number of other recently appointed functionaries, have their work cut out. The ease with which Israel incapacitated Iran’s territorial defence capabilities have served to undermine somewhat the reputation that the IRGC had earned during the Iraq War. Crucially, in the years after the Iraq War, that reputation helped the IRGC gather considerable wealth, economic influence, and substantial leverage over the Islamic Republic in the name of safeguarding the regime. Israel’s penetration of Iranian territorial defence and decimation of a segment of its upper tiers is raising the question about how useful has that investment been. Mohammad Pakpour may still use the success of Iranian ballistic missile strikes on Israel to salvage the reputation of his organisation and press for repair and acceleration of Iranian nuclear programme, and press hard the case for building the bomb – but it would not be an easy task.

Of course, the reformist-pragmatist combination presently at the helm of the government in Tehran may readily close ranks with the IRGC and the nuclear lobby out of consideration for national defence, and decide to go for the bomb right away by pulling out of NPT – as the hardliner-IRGC dominated Majlis (parliament) already seems to be clamouring for. But going down that path would expose Iran to further sanctions, and greater regional turmoil. Given the track record of the reformists, that is an unlikely trajectory.

By contrast, the reformists might want to question the capability of the IRGC in the light of their demonstrable weakness, and favour rebuilding Iranian nuclear capabilities without weaponising – yet again – and pursue the diplomatic path to safeguard the Islamic Republic instead. However, Tehran would probably not want to return to the negotiation table readily (for that could indicate admission of weakness), especially not without a proper audit of the damages to its nuclear infrastructure. Once that audit is done, the less damage the nuclear infrastructure is found to have sustained, the stronger would be the diplomatic hand that Tehran might want to play – remaining as close to the JCPOA as possible, with Tehran’s right to nuclear enrichment programme and its ballistic missile programme being the two red lines. Tehran would certainly want to have the economic sanctions removed, but it would not want to become the next Libya.

Conclusion

The Twelve Day War between Israel and the Islamic Republic of Iran has made the Middle East more combustible than it had been so far. The attack on an NPT-signatory state that is yet to develop nuclear weapons by one signatory nuclear power and one non-signatory nuclear power has virtually guaranteed Tehran going nuclear at some time in the near future. It would require a lot of patience and goodwill in prospective nuclear talks to desist Iran from following that path – two qualities that the Trump administration does not seem to have much of. Hence, unless the Israeli state simmers down from its politics of rage and behaves less like a bull-in-a-china shop, further and rolling conflicts in the region have become far more likely than previously, Tehran is certain to remain ranged against Tel Aviv.

(The paper is the author’s individual scholastic articulation. The author certifies that the article/paper is original in content, unpublished and it has not been submitted for publication/web upload elsewhere, and that the facts and figures quoted are duly referenced, as needed, and are believed to be correct). (The paper does not necessarily represent the organisational stance... More >>