Mr. Fakhrizadeh was an academic, but a series of classified reports, notably a lengthy 2007 assessment done by the C.I.A. for the George W. Bush administration, said the academic role was a cover story. In 2008, his name was added to a list of Iranian officials whose assets were ordered frozen by the United States.
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 as they try to make a warhead small enough to fit atop a missile and make it survive the rigors of re-entry into the atmosphere.
Iran has always denied it was seeking a nuclear weapon, insisting its production of nuclear material was purely for peaceful purposes. 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 his involvement.
Shortly thereafter, Prime Minister Benjamin Netanyahu of Israel 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.
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.”
“And also, not coincidentally,” Mr. Netanyahu added, showing a picture that appeared to be Mr. Fakhrizadeh — there are only a handful of images of him that have been published — “many of S.P.N.D.’s key personnel worked under Fakhrizadeh on Project Amad.”
The killing could complicate Biden’s handling of the Iran nuclear deal.
Mr. Fakhrizadeh’s killing could have broad implications for the incoming Biden administration. It is bound to set off a sharp reaction in Iran, as did the American attack on Jan. 3 that killed Qassim Suleimani, the Iranian major general who ran the elite Quds force of the Islamic Revolutionary Guards Corps.