Craig Whitlock • The Washington Post

The U.S. military was closely tracking a one-eyed bandit across the Sahara in 2003 when it confronted a hard choice that is still reverberating a decade later. Should it try to kill or capture the target, an Algerian jihadist named Mokhtar Belmokhtar, or let him go?

Belmokhtar had trained at camps in Afghanistan, returned home to join a bloody revolt and was about to be blacklisted by the United Nations for supporting the Taliban and al-Qaida. But he hadn’t attacked Americans, not yet, and did not appear to pose a threat outside his nomadic range in the badlands of northern Mali and southern Algeria.

Military commanders planned to launch airstrikes against Belmokhtar and a band of Arabs they had under surveillance in the Malian desert, according to three current and former U.S. officials familiar with the episode. But the ambassador to Mali at the time said she vetoed the plan, arguing that a strike was too risky and could stir a backlash against Americans.

Since then, Belmokhtar has gradually built a Qaida-branded network while expanding his exploits as a serial kidnapper, smuggler and arms dealer. Last month, his group, Signatories in Blood, took dozens of hostages at a natural-gas complex in Algeria. At least 38 foreign captives were killed, including three Americans.

In addition to raising his global profile, the spectacular attack turned Belmokhtar into a symbol of how the United States over the past 10 years bungled an ambitious strategy to prevent al-Qaida from gaining a foothold in North and West Africa.

The U.S. government has invested heavily in counterterrorism programs in the region, spending more than $1 billion since 2005 to train security forces, secure borders, promote democracy, reduce poverty and spread propaganda.

The strategy was portrayed as a sobering lesson from the costly invasions of Afghanistan and Iraq. By stabilizing weak African countries, the goal was to keep al-Qaida out and obviate the need to send U.S. combat forces into the Sahara.

Despite those efforts, Belmokhtar’s group and a hazy array of other jihadist factions and rebellious tribesmen seized control of the northern half of Mali last year. In March, a U.S.-trained Malian officer carried out a coup, further plunging the country into chaos.

“We had this great program and we put hundreds of millions of dollars into it, and it failed. Why did it fail?” said a member of the U.S. Special Operations Forces who worked in Africa until he retired last year. “Fundamentally, we missed the boat.”

Todd Moss, deputy assistant secretary of state for African affairs from 2007 to 2008, blamed “a wholly inadequate policy response.” He said U.S. officials placed their faith in a flawed model to promote development and build institutions, especially in northern Mali, a Texas-sized territory with little government presence.

“There was no consensus on the size or seriousness of the threat,” he added. “We were looking through both civilian and military rose-colored glasses. And that should give us pause as we try to figure out how to move forward.”

By 2003, U.S. officials were becoming alarmed about the potential for Islamist extremists to establish a haven in North or West Africa.

Radicals who failed to topple the Algerian government in the 1990s had moved deep into the Sahara, hiding in the hinterlands of impoverished countries such as Mali, Mauritania and Niger, where they turned to smuggling and other criminal rackets.

Among them was a former paratrooper known as Abderrazak Al Para, who kidnapped 32 Europeans and collected $6 million in ransom.

No American hostages were involved in that kidnapping, but the incident drew the attention of commanders at the U.S. European Command in Stuttgart, Germany. Using satellite imagery and other sources, the U.S. military tracked Al Para and shared the intelligence with African governments, which pursued him across the desert. After an epic chase, he was captured in Chad.

Around the same time, the U.S. military also started to track Belmokhtar and floated a plan to fire missiles into an Arab camp in northern Mali. Vicki Huddleston, then the U.S. ambassador to Mali, said she blocked the operation. It was unclear if Belmokhtar was actually present, and he was considered a minor figure, she recalled in an interview.

“I said no. First, you don’t know who these people are, and second, it’s a bad idea,” she said. “We had a big fight over this.”

The four-star Air Force general in charge of the operation, Charles Wald, now retired, acknowledged that he wanted to nab Belmokhtar, but insisted airstrikes were not a serious option. He said the U.S. military wanted to share intelligence and gear with Algeria and Mali so they could arrest or kill Belmokhtar, but that civilian U.S. leaders refused. “The answer at that time was, ‘Not our business.’”

Wald is still angry at what he sees as a missed opportunity, saying the military had “about a thousand” chances to get the bandit. “We allowed Belmokhtar to become larger than life,” he said in an interview. “He was well within reach,” he added. “It would have been easy.”

Ten years later, the general and ambassador still disagree over whether they should have seized that chance to eliminate Belmokhtar. But they concur the dispute foreshadowed flaws in the forthcoming U.S. strategy to prevent al-Qaida from planting roots in the region.

“I’m really frustrated right now because I think we blew it,” Wald said, speaking in general about U.S. counter-terrorism policy in Africa. “We’ve gone backwards, frankly.”

Huddleston was later appointed by President Barack Obama as the top Africa policy official in the Pentagon, where she earned a reputation among her former diplomatic colleagues as a zealous hawk on security matters.

She said the U.S. government never overcame divisions over how aggressively it should respond to the emergence of al-Qaida’s North African affiliate. The Pentagon was often too eager to take direct military action, she added, while the State Department was too willing to tolerate al-Qaida’s presence.

“The issue has come up again and again,” said Huddleston, who retired from the Pentagon at the end of 2011. “The Defense Department wanted to help the countries in the region to confront the threat, and State wanted to contain.”

The failure to keep Islamist extremists from taking over northern Mali was not for lack of money or attention from Washington.

In 2005, the U.S. government started the Trans-Sahara Counterterrorism Partnership — the innovative, $1 billion collection of programs designed to prevent the spread of radicalism. It delivered humanitarian aid and security assistance to 10 countries in North and West Africa, drawing on the combined resources of the military, the State Department and the Agency for International Development.

The partnership was dogged by problems from the outset, however, as U.S. agencies squabbled internally and struggled to understand an unfamiliar cultural and political terrain.