WASHINGTON — The assassination of the scientist who led Iran’s pursuit of a nuclear weapon for the past two decades threatens to cripple President-elect Joseph R. Biden Jr.’s effort to revive the Iran nuclear deal before he can even begin his diplomacy with Tehran.

And that may well have been a main goal of the operation.

Intelligence officials say there is little doubt that Israel was behind the killing — it had all the hallmarks of a precisely timed operation by Mossad, the country’s spy agency. And the Israelis have done nothing to dispel that view. Prime Minister Benjamin Netanyahu has long identified Iran as an existential threat, and named the assassinated scientist, Mohsen Fakhrizadeh, as national enemy No. 1, capable of building a weapon that could threaten a country of eight million in a single blast.

But Mr. Netanyahu also has a second agenda.

“There must be no return to the previous nuclear agreement,” he declared shortly after it became clear that Mr. Biden — who has proposed exactly that — would be the next president.

Mr. Netanyahu believes a covert bomb program is continuing, until yesterday under Mr. Fakhrizadeh’s leadership, and would be unconstrained after 2030, when the nuclear accord’s restraints on Tehran’s ability to produce as much nuclear fuel as it wants expires. To critics of the deal, that is its fatal flaw.