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As Threat of Another Israel/Iran Conflict Rises, Will Israel Target Ali Khamenei?

A lot of Israeli analysts and officers are openly saying they think another clash is likely, because Iran will feel pressure to prove it can still impose costs after the damage to its nuclear program and leadership.

1. How Israel will likely approach the next round

If you look at Israeli doctrine and behavior over the last 15–20 years, a few themes show up:

Surprise and novelty are part of the strategy.

Their core strategic goals are pretty consistent:

Next time is likely to be multi-domain again, not just “more of June 2025.” I’d expect some mix of:

They’ll also be more conscious of blowback. That last war did serious damage to Iran’s nuclear program, but it also brought huge criticism, economic shocks, and a non-zero chance of miscalculation spiraling.

So the Israeli leadership will be asking:

In June, Israel killed scores of scientists and IRGC generals, but it stopped short of taking out the Supreme Leader (either because it did not know his location, or because Donald Trump stopped that from happening to prevent a much larger conflict.

Understanding the Many Paradoxes of Iran

To be clear, I do not condone the killing of anyone on either side of the conflict, and despite my criticisms of Iran’s foreign policy and domestic laws that impede on human rights, I do NOT condone the taking out of any head of state as – ceteris paribus – that almost always ensures a wider, escalating conflict. My idealistic but admittedly “saadeh” solution would be some form of amnesty where a combination of Khamenei’s old age, Iran’s weakening electric and water infrastructure, decimated currency, and the spectre of sustained conflict with Israel and the USA would induce an end of the theocratic nature of the republic, and a form of amnesty which would initiate a process that would give the people what it ultimately wants: an end of Velayat e Faqih. Of course, in reality, Khamenei will fight tooth and nail to stay in power, and if he were to die of a natural cause, the most likely denouement is a power struggle between the clerics and the IRGC. I may be the lone Iranian that simply wants no more Iranian deaths of any ideology, whereas many of those living inside are simply done with the regime, and would try Khamenei in court if they had their way.

Iran, however, is unique in that a minority of clerics control via the IRGC the majority of the nation’s 90 million citizens, mostly secular, many of whom support a restoration of Iran’s constitutional monarchy and the Pahlavi dynasty by way of the exiled crown prince, Reza Pahlavi – ironically, it is the Mullahs’ and Iran’s decline since 1979 that has popularized the monarchy and tainted the concept of republic. While Arab states are friendly with America when the Arab street is critical of it due to the US’ support for Israel, Iranians are generally very pro-West and the people love America (its culture) whereas its regime views it as the Great Satan, casting itself not just as savior of Islam, defender of Palestine, but the stalwart against Western hegemony. This is just one of many misconceptions about Iran.

However, with America having effectively helped topple Pahlavi’s father Mohammad Reza Pahlavi (aka Aryamehr), it is awkward for them to put their support behind his son, which explains why some politicians (usually paid) have promoted the MEK, a group that is even less popular than the current rules. Iranians are also wary of US normalizing relations with the regime, urging Donald Trump to say “no deal” to Tehran, as a deal would effectively serve as a possible death blow to their hopes of a return of the monarchy (given Pahlavi’s age). In reality, Iran has had dynasties lasting longer than most other empires, so whether the Mullahs continue their 45 year-rule for another 45 days, 4 or 45 years, history does not have many examples of a minority ruling over a majority forever. For those curious, as an entrepreneur, my default preference is not usually a heredity-based system, but in light of the foregoing, I certainly understand why so many Iranians would favor a monarchy (secular, democratic, etc) and not a theocracy that is a republic in name, but effectively autocratic.

2. Would Israel assassinate the Supreme Leader personally

As Israel was stopped short of killing the Supreme Leader of the Islamic Republic, the Ayatollah Ali Khamenei last time, it was also alarmed by Iran’s overwhelming showering of missiles across the Jewish State. As such, it understands that repeating the same tactic – eliminating scientists and IRGC members alone while Iran responds even more fervently – will not meet its ultimate goal of eliminating the threat of the regime that refers to it as the Little Satan. And, after 10/7, it is clear that Israel does not care about international reaction and prioritizes its own long term safety. The only way that is achievable, in Israel’s eyes is by taking out the so-called head of the state, quickly.

Talking analytically, not normatively:

But going after Khamenei himself, a Marja, or “source of emulation” and rank far higher than an Ayatollah (despite the irony that originally, Khamenei did not have the credentials to be an ayatollah replacing Ruhollah Khomeini) would indeed be unprecedented.

Escalation level: Killing the supreme leader is closer to decapitating a regime than to a “normal” targeted killing. That’s the kind of move that could realistically trigger:

International law and politics: Targeting a sitting head-of-state-level figure is legally and politically radioactive.

Israel already walks a fine line with its pre-emptive doctrine; this would cross into territory that many of its allies might not be willing to defend.

Risk vs reward: From a cold strategic perspective, it’s not obvious that killing Khamenei solves Israel’s problems.

Signals from Iran itself: Iranian officials have recently been talking about “plots” against Khamenei and blaming Israel and the US, but that’s as much propaganda and internal control as it is intelligence. It shows Tehran worries about regime security, but it doesn’t prove Israel is actually planning that.

So is it theoretically something military planners think about as a contingency? Of course.

Is it a “realistic primary option” in terms of likely Israeli policy? Most serious analysts would probably rank it as low probability, compared to:

In other words: it’s unlikely to be the default “next step” after the 12-day war, because the escalation and uncertainty are so huge, but therein lies the ultimate paradox of the Islamic Republic: as a Shia nation, Iran is seen with suspicion by the largely Sunni Arab world. Despite Iran’s tens of billions of investment in its Axis of Resistance, those proxies ultimately did not serve Tehran’s interests, and the elimination of a Shia head of state, while sure to draw the ire and outrage of many across the Ummah, will likely not cause a radical escalation because when said and done, Muslim states did not come to the aid of Palestinians (the supposed beacon and guiding light of the entire resistance narrative), so it’s unlikely that the end of the Islamic regime will be seen as a bad thing altogether.

Paradoxically, Iran’s prioritization of Palestinians over Iranians may prove to be the self inflicted wound that ends its rule over Iranians.

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