The assassination of Mohsen Fakhrizadeh, the Iranian nuclear scientist considered the father of the Islamic Republic's nuclear weapons programme, has been widely attributed to Israel, which has not claimed responsibility. Different theories have been floated about why Israel would conduct this operation now, if indeed it did.

One holds that it is an Israeli attempt to box in President-elect Joe Biden before he takes office, making it impossible for him to rejoin the Iran nuclear deal negotiated during the Obama-Biden administration, as he has pledged to do if Iran returns to compliance.

Another theory is that killing Fakhrizadeh would have been consistent with Israel's longstanding efforts to roll back Iran's nuclear programme, which have included covert operations. Such an operation would probably have to have been planned long ago and conducted when the opportunity arose. A third theory, which straddles the other two, suggests that Israel took an action when it had a green light from the Trump administration, while preparing for a new phase in its struggle with Iran once Biden takes office.

These theories aren't mutually exclusive, and some combination of the three may well apply. What matters now in the US-Israel alliance is whether the administration of Israeli Prime Minister Benjamin Netanyahu recognises that it has an opportunity to craft a common Iran strategy with a Biden administration. And that the Biden administration sees it should be open to Israeli perspectives and analysis if it wants to work together with Israel on the threat posed by Iran. Israel can't contain Iran alone. And it doesn't have to.

In a recent interview, Biden expressed his intention to return the United States to the Joint Comprehensive Plan of Action — the 2015 nuclear agreement between Iran and the United States, Britain, France, Germany, China and Russia that President Trump pulled the United States out of in 2018 — and the deal's nuclear-restrictions-for-sanctions-relief formula, if Iran complies with its terms. Last month, Netanyahu delivered an opposing message deemed to be directed at Biden: "There can be no going back to the previous nuclear agreement."

Taken together, the statements might appear to set up an impasse at the start of the new US administration that could damage the relationship between allies. But the United States and Israel have managed differences on Iran policy before. Although there was a serious rift over the JCPOA, including Netanyahu's 2015 speech in Congress criticising the deal, for several years before that, the two countries had co-ordinated effectively on Iran: sharing intelligence, co-operating on sanctions design and enforcement, and using or preparing both covert and military options. It was only in the later stages of negotiations with Iran that divergent US and Israeli perspectives overtook previous understandings.

Differences in the sizes of the two countries, their respective military capabilities and their geographic proximity to the threat from Iran meant that Israel and the United States, unsurprisingly, had different levels of risk tolerance over the agreement's provisions.

However, some members of Israel's security establishment took a more nuanced view than Netanyahu's flat rejection. Amos Yadlin, a former head of Israeli military intelligence, has argued that the JCPOA had pros in the early years of its term, with the time bought by the strictly enforced limits on Iran's nuclear programme, and cons in the later years, as those restrictions expire, allowing Iran to accelerate its nuclear programme.

Netanyahu was unable to block the deal. But after Trump's election in 2016, the prime minister found a president who shared his criticisms and who was willing to pull out of the deal.

But even from Israel's perspective, the results of Trump's "maximum pressure" approach to Iran have been mixed. US-imposed sanctions have hurt Iran's economy, but Iran has also resumed enriching uranium and is, as Biden says, "moving closer to the ability to be able to have enough material for a nuclear weapon". Trump's approach has drawn cheers from Israel and the Arab Gulf states but has damaged the international coalition on which the JCPOA was based.

Biden's victory means that approach will change. Israel should make its case in early, high-level consultations between the two governments. But it will have no ability to dictate US policy, so it will also need to be prepared for Biden to attempt to re-enter the deal. That means developing a common strategy to prevent Iran from acquiring nuclear weapons that looks beyond the remaining years of the JCPOA and draws on all the tools — diplomatic, economic, covert and military — in each of the two nations' toolboxes.

The Biden Administration will need to take into account that Israel will continue to view an Iranian nuclear weapon as an existential threat, and, like any sovereign nation, will act as it believes necessary to defend itself. On this point, Biden and his secretary of state-designate, Antony Blinken, longtime supporters of Israel's security, have no illusions. The United States will also benefit if the dialogue with Israel expands beyond the narrow question of the JCPOA, where there will certainly be disagreement.

For one thing, that question may be moot. By the time Biden takes office, Iran may be so far out of compliance that a return is impossible. He will have to consider whether any sanctions Trump deployed provide leverage to get Iran to agree to extend the JCPOA's terms. Even if Biden removes them, he will retain the ability to threaten their reimposition if needed, and Iran knows they have bite. Israel should consider what form an extension of the JCPOA can take that would provide assurance that Iran will remain non-nuclear while buying time for a more comprehensive resolution.

Biden's team also understands that even if Iran's nuclear potential may be the gravest threat it poses, its other aggressive activities — developing advanced ballistic missiles; supplying regional proxies such as Hezbollah and Yemen's Houthi rebels; and attempting to encircle Israel with a ring of precision-guided missiles — must also be addressed. Indeed, earlier this year, Jake Sullivan, Biden's national security adviser-designate, and Daniel Benaim, a Biden Middle East policy adviser, called for a "structured regional dialogue" that could address Iran's non-nuclear threats in parallel with renewed nuclear talks. Such diplomacy, augmented by sanctions and other measures when required, should ensure that Israel's interests are represented, whether or not Israel sits at the table.

A comprehensive solution to the problem of containing Iran should be the focus of this joint US-Israeli effort. Biden has called for a longer, stronger agreement that will ensure Iran does not achieve a nuclear weapon for the long term, which would mean stricter inspection protocols and application to other dangerous technologies, such as ballistic missiles. He has made clear that he does not tolerate Iran's dangerous regional role and accepts Israel's need to act against threats such as Iranian military installations in Syria. These positions, and the mixture of pressures and incentives deployed to influence Iranian calculations towards a set of long-term understandings, are potential points of convergence with Israel and other regional players.

At the end of the day, the United States and Israel do not have to agree on everything, but it's in their mutual interest to co-ordinate their approaches on Iran. Israel has the capability and the political will to conduct operations akin to the Fakhrizadeh killing. But it isn't tenable for Israel to confront Iran without limits if doing so puts it in direct opposition to the strategy of a friendly US administration that is pursuing the same strategic goal of preventing an Iranian nuclear weapon for the long term, while defending other key US interests.

Those in both countries who are expecting an inevitable clash between allies should pause and think. The United States and Israel will continue to share common goals: an Iran that is non-nuclear and that does not threaten and harm its neighbours. A wide range of tools, in the short, medium and long term, are available for a joint strategy to achieve them.

A commitment early on to overcome disagreements on tactical questions, and to focus together on common strategic objectives, will be better for the US-Israel alliance and a more effective way to contain Iran.

• Daniel Shapiro is a distinguished visiting fellow at the Institute for National Security Studies at Tel Aviv University. He served as US ambassador to Israel from 2011 to 2017