The killing of Ayman al-Zawahri may have more resonance for Americans who lived through the September 11, 2001, terrorist attacks that he plotted along with Osama bin Laden, but the intention in snuffing him out was in a sense less about the past than the future. 

President Biden said from the White House on Monday that al-Zawahri “will never again, never again, allow Afghanistan to become a terrorist safe haven because he is gone and we’re going to make sure that nothing else happens.”

Just desserts came tardily but definitively to the terrorist. The Al Qaeda leader evaded U.S. capture for 21 years after the suicide airliner attacks that destroyed the World Trade Center in many ways changed New York, America, and its relations with the rest of the world. Many may not remember al-Zawahri’s name but can recognize his face, more than two decades later: a man in glasses, slightly smiling, invariably shown in photos by the side of bin Laden as the two arranged the attacks on America.

As the sun was rising in Kabul on Sunday, two Hellfire missiles fired by a U.S. drone ended Ayman al-Zawahri’s decade-long reign as the leader of Al Qaeda. The seeds of the audacious counterterrorism operation had been planted over many months.

U.S. officials had built a scale model of the safe house where al-Zawahri had been located, and brought it into the White House Situation Room to show President Biden. They knew al-Zawahri was partial to sitting on the home’s balcony.

They had painstakingly constructed “a pattern of life,” as one official put it. They were confident he was on the balcony when the missiles flew, officials said.

Years of efforts by U.S. intelligence operatives under four presidents to track al-Zawahri and his associates paid dividends earlier this year, Mr. Biden said, when they located Osama bin Laden’s long-time no. 2 — a co-planner of the September 11, 2001, terrorist attacks on the U.S. — and ultimate successor at the house in Kabul.

Bin Laden’s death came in May 2011, face to face with a U.S. assault team led by Navy SEALs. Al-Zawahri’s death came from afar, at 6:18 a.m. in Kabul.

His family, supported by the Haqqani Taliban network, had taken up residence in the home after the Taliban regained control of the country last year, following the withdrawal of U.S. forces after nearly 20 years of combat that had been intended, in part, to keep Al Qaeda from regaining a base of operations in Afghanistan.

But the lead on his whereabouts was only the first step. Confirming al-Zawahri’s identity, devising a strike in a crowded city that wouldn’t recklessly endanger civilians, and ensuring the operation wouldn’t set back other U.S. priorities took months to fall into place.

That effort involved independent teams of analysts reaching similar conclusions about the probability of al-Zawahri’s presence, the scale mock-up and engineering studies of the building to evaluate the risk to people nearby, and the unanimous recommendation of Mr. Biden’s advisers to go ahead with the strike.

Mr. Biden ordered what officials called a “tailored airstrike,” designed so that the two missiles would destroy only the balcony of the safe house where the terrorist leader was holed up for months, sparing occupants elsewhere in the building.

On July 25, as Mr. Biden was isolated in the White House residence with Covid-19, he received a final briefing from his team.

Each of the officials participating strongly recommended the operation’s approval, the official said, and Mr. Biden gave the sign-off for the strike as soon as an opportunity was available.

That unanimity was lacking a decade earlier when Mr. Biden, as vice president, gave President Obama advice he did not take — to hold off on the bin Laden strike, according Mr. Obama’s memoirs.

The opportunity came early Sunday — late Saturday in Washington — hours after Mr. Biden again found himself in isolation with a rebound case of the coronavirus. He was informed when the operation began and when it concluded, the official said.

A further 36 hours of intelligence analysis would follow before U.S. officials began sharing that al-Zawahri was killed, as they watched the Haqqani Taliban network restrict access to the safe house and relocate the dead Al Qaeda leader’s family. U.S. officials interpreted that as the Taliban trying to conceal the fact they had harbored al-Zawahri.

After last year’s troop withdrawal, the U.S. was left with fewer bases in the region to collect intelligence and carry out strikes on terrorist targets. It was not clear from where the drone carrying the missiles was launched or whether countries it flew over were aware of its presence.

The U.S. official said no American personnel were on the ground in Kabul supporting the strike and the Taliban was provided with no forewarning of the attack.

In remarks 11 month ago, Mr. Biden had said the U.S. would keep up the fight against terrorism in Afghanistan and other countries, despite pulling out troops. “We just don’t need to fight a ground war to do it.”

“We have what’s called over-the-horizon capabilities,” he said.

On Sunday, the missiles came over the horizon.