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President Barack Obama's administration has decided to keep U.S. military bases and conduct counterterrorism operations in Afghanistan after bringing the longest war in America's history there to an end next year. But its decision, centered on keeping a substantial residual military force, risks locking the U.S. post-2014 in a low-intensity but never-ending war in that lawless, rugged country.

The Bilateral Security Agreement (BSA) reached between Washington and Afghan President Hamid Karzai last week defines a U.S.-led counterterrorism and training mission involving up to 12,000 NATO troops, mostly American, and lasting "until the end of 2024 and beyond" unless terminated with two years' advance notice. This will mean virtually indefinite U.S. troop presence in Afghanistan and include a mandate, as the text says, to "conduct combat operations."

Mr. Obama's decision in favor of strong military basing in Afghanistan – where there are currently about 45,000 American troops – stands in sharp contrast to his earlier action in pulling out all U.S. forces from Iraq after a decade-long American occupation of that country.

Afghanistan's Loya Jirga, or assembly of tribal leaders, put its imprimatur last Sunday on the BSA, which grants the U.S. important concessions, including a controversial immunity for American troops from Afghan law and permitting U.S. Special Operations forces to conduct anti-terrorism raids on private Afghan homes. Washington leveraged the more than $4-billion annual security aid it has promised to get these provisions in.

However, rejecting Washington's demand that the deal be signed by the year-end, Mr. Karzai – concerned over leaving behind a legacy as the main facilitator of a long-term U.S. military presence – has threatened to delay that action until his successor is elected in next April's presidential election. Washington has warned that it would be forced to begin planning for a complete withdrawal of U.S. forces at the end of 2014 if Karzai did not sign the BSA by this year-end.

In any event, the U.S. needs a separate deal with the Afghan Taliban, or else its military bases would likely come under intense insurgent attacks post-2014. Indeed, the Obama administration is seeking to cut a broader deal with the Taliban to allow it to "honorably" end combat operations next year – an objective that has prompted it to kiss and make up with Pakistan, which shelters the top Taliban leadership.

The U.S. recently restored its $1.6-billion aid flow to Pakistan, which had been blocked because that country never came clean over who helped Osama bin Laden hide for years in a military garrison town near its capital, Islamabad.

Imperial Britain created many unnatural political constructs, including two countries that have searched vainly to shape a national identity – Afghanistan and Pakistan (or "Afpak" in Washingtonese). The Afpak belt, for the foreseeable future, is likely to remain a bastion of transnational terrorists, with the Durand Line legacy making Afghanistan and Pakistan virtual Siamese twins.

The Durand Line – arbitrarily bisecting ethnic Pashtun and Baloch homelands – is the Afghan-Indian border the British demarcated in 1893 and which later became the frontier between Afghanistan and Pakistan. Decades after Pakistan's creation in 1947, the Durand Line remains a mythical border, with successive Afghan governments refusing to recognize it and the validity of the porous line challenged by daily cross-frontier movement of people and extremists.

America's post-2014 strategy risks perpetuating the same mistake that has led it to falter in the ongoing 12-year war, which has cost it nearly a trillion dollars and killed tens of thousands of people – limiting its military operations to Afghanistan in a binational region that has become a single geopolitical unit, with militant sanctuaries, command-and-control structure and support infrastructure for the Afghan insurgency located on the other side of the Durand Line. Terrorism and insurgency have never been defeated anywhere in the world without cutting off transboundary sustenance and support.

In recent years, the U.S. has carried out from Afghanistan a series of air and drone strikes on Pakistan's tribal Waziristan region, targeting the nemesis of the Pakistani military – the Pakistani Taliban. But to preserve the option of reaching a Faustian bargain with its main battlefield opponent – the Afghan Taliban – the U.S. has not carried out a single air, drone or ground attack against that militia's leadership, which is ensconced in Pakistan's sprawling Baluchistan province, located to the south of Waziristan.

In seeking to co-opt the Afghan Taliban, the Obama administration seems unconcerned that it is bestowing legitimacy on a terrorist militia which enforces medieval practices in the areas currently under its control and which, according to a recent United Nations report, raised $155-million last year from illicit opium production.

Even if the administration succeeded in cutting a deal with the motley Afghan Taliban, powerful factions within the militia may not honor it.

Mr. Obama, who had earlier promised to bring all troops home, has not explained how a residual American force, even if sizable, would make a difference in Afghanistan when a much larger force is staring at defeat.

A long-term U.S. military presence, besides compelling Washington to work with Afpak elements that have a long record of duplicitous conduct, could boost the militant cause. Yet if the U.S. completely washed its hands of Afghanistan, Afpak could sink deeper into a jihadist dungeon. The U.S. faces difficult choices, compounded by the administration's failure to clarify strategic goals.

With violence soaring, Afpak's future remains more uncertain than ever. There is considerable risk of an Iraq-style "soft" ethnic partition of Afghanistan.

The worst scenario would be the Taliban's return to power in Kabul, with the thuggish militia's control extending across much of Afghanistan. That would not only unleash a fresh reign of Islamist terror but also allow transnational terrorists to reestablish a major operational base, thereby sucking U.S. forces into bloody counterterrorism missions. It would be as if history had come full circle.

Brahma Chellaney is a geostrategist and author.