A Reaper in Seychelles, which unlike some of the other bases, has been previously acknowledged as a site for drones. (Maj. Eric Hillard — U.S. Africa Command)

In assembling a constellation of secret drone bases around Yemen and Somalia, the United States is trying to eliminate refuges for al-Qaeda and its affiliates. But it’s also trying to do something else: avoid the mistakes of the past.

When al-Qaeda fled Afghanistan into Pakistan in 2001 and 2002, it took years before the CIA had assembled a drone program capable of putting the terrorist network under pressure. That delay, and costly deals for air-basing access in neighboring countries, allowed al-Qaeda to flourish.

When the new bases are complete, the United States will have at least four drone airstrips in the Horn of Africa region: a long-standing military base in Djibouti; a secret new CIA facility being built in the Arabian Peninsula; an installation on the Seychelles; and a fourth facility in Ethiopia.

The bases will be used to target al-Qaeda affiliates in Yemen and Somalia, but also position the United States to patrol other areas to which militant groups might migrate.

“We’re posturing with the right capabilities [in Africa] to be able to move against targets if they start to develop rather than wait four or five years like we did in Pakistan,” said a former senior U.S. military official familiar with special operations mission in both regions. “We’ve learned a lot of lessons in the last eight or nine years with respect to basing rights.”

Officials said that it costs a lot more to build the bases when the need is urgent and the United States has limited options. “A lot of bases [around Afghanistan] we had to pay a hefty sum of money to operate out of,” said the former official who requested anonymity because he is not authorized to speak on the record. “You don’t want all your eggs in one basket.”

That’s one lesson that U.S. officials have learned the hard way. Amid persistent tensions between Islamabad and Washington, Pakistani officials have repeatedly threatened to kick the CIA off their bases — a move that would likely have a severe effect on the agency’s ability to target key members of al-Qaeda.