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That same year, his activities were disclosed in an unclassified briefing by the I.A.E.A.’s chief inspector. Later, it became clear that he ran what the Iranians called Projects 110 and 111 — an effort to tackle the most difficult problems bomb designers face in creating a warhead small enough to fit atop a missile and make it survive the rigors of re-entry into the atmosphere.

He stayed out of sight for years. But an Israeli operation in early 2018 that stole a warehouse full of Iranian documents about “Project Amad,” what the Iranians called the nuclear weapons effort 20 years ago, included documents about Mr. Fakhrizadeh, and at least one handwritten by him, the Israelis contended.

Shortly thereafter, Mr. Netanyahu singled out Mr. Fakhrizadeh in a televised presentation, when he described the secret Israeli operation to seize the archive. Iran had lied about the purpose of its nuclear research, he charged, and he identified Mr. Fakhrizadeh as the leader of the Amad program.

Iran said Mr. Netanyahu’s presentation was fiction.

Israeli officials, later backed up by American intelligence officials who reviewed the archive, said the scientist had kept elements of the program alive even after it was ostensibly abandoned. It was now being run covertly, Mr. Netanyahu argued, by an organization within Iran’s defense ministry known as S.P.N.D. He added: “You will not be surprised to hear that S.P.N.D. is led by the same person who led Project Amad, Dr. Fakhrizadeh.”

The assassination comes at a time of greatly heightened tensions between Iran and the Trump administration. Mr. Trump was dissuaded from striking Iran just two weeks ago, after his aides warned it could escalate into a broader conflict during his last weeks in office.

Mr. Trump had asked senior advisers in an Oval Office meeting on Nov. 12 whether he had options to take action against Iran’s main nuclear site at Natanz in the coming weeks. Days later, Mr. Pompeo visited Israel on what could be his last trip there in office.