With the impending drawdown of U.S. forces, a largely overlooked conflict has the potential to explode.


When American special forces plucked the second in command of the Pakistani Taliban from the hands of Afghan officials this October, they laid bare the extent of a largely covert war between Afghanistan and Pakistan that has been going on for several years. With a drawdown – perhaps even to zero – of U.S. troops from Afghanistan next year, the secret war might just become an open one.

The capture of Latif Mehsud proved to be an embarrassment for the Afghans, and a vindication for Pakistan, which has long complained that the Pakistani Taliban – called the Tehrik -e-Taliban (TTP) – receives support from Karzai’s government. Afghanistan and the United States, for their part, have laid the blame for a 12-year insurgency at Pakistan’s feet, saying its intelligence agencies support the most effective insurgency group, led by Jalaluddin Haqqani.

Latif Mehsud was a close confidant of Qari Hussain, who was one of the candidates to take over the TTP after the killing of its leader, Baitullah Mehsud, by an American drone strike in 2009. When Hussain was similarly eliminated in October 2010, Latif took over as the TTP’s second in command, operating under its leader, Hakimullah Mehsud. (The two Mehsuds are from the same tribe, but not closely related.) Latif’s capture provided the intelligence the U.S. needed to kill Hakimullah, in a drone strike just a few weeks later.

Latif spent much of his time since 2010 between Afghanistan and Pakistan, and it is believed he was a conduit for funding to the TTP. It now appears some of that funding might have come from Afghanistan’s intelligence agency, the National Directorate of Security (NDS).

On October 5, Latif was being taken by Afghan officials to a meeting with agents from the NDS when American special forces stopped his convoy, taking Latif to Bagram, where the U.S. runs a prison of its own.

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The TTP has been blamed for tens of thousands of deaths in Pakistan, in brazen attacks on government and civilian targets alike that began in 2007. The group has also claimed responsibility for an attempted car bombing in New York City in 2010.

It’s not the kind of group Karzai’s government would ostensibly want to be associated with.

Yet, the president’s spokesperson, Aimal Faizi, openly told reporters the NDS had been working with Latif “for a long period of time.” Latif, Faizi said, “was part of an NDS project like every other intelligence agency is doing.”


The Afghans evidently decided it was time to cultivate their own proxies for leverage with Pakistan.

The Haqqani insurgent network, which has inflicted the most damage on Afghan and U.S. forces, is based in North Waziristan, where Pakistan has thousands of troops stationed, but has held off on trying to clear the area of militants. It is also home to a number of senior TTP members, and has borne the brunt of American drone strikes.

“The Haqqani network…acts as a veritable arm of Pakistan’s Inter-Services Intelligence Agency,” Admiral Mike Mullen, the then top American military official told Congress in 2011. U.S. officials were irate, saying as far back as 2008, they had tracked the communication lines of Haqqani militants during attacks in Kabul to control rooms in Pakistan, which was directing the operation in real time. None of the evidence was made public, but the NDS was apparently motivated to offer funding to the TTP through operatives like Latif Mehsud. The TTP has a stated goal of toppling the Pakistani state, just as the Afghan Taliban hope to topple the Karzai government.

There is also speculation the NDS might be carrying out an assassination program of its own in Pakistan. In an embarrassing development for Pakistan, a gunman shot dead Nasiruddin Haqqani, a top facilitator of the insurgent group, in the Pakistani capitol of Islamabad last month.

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Both the Afghan Taliban and the TTP operate across the Afghanistan-Pakistan border, each country turning a blind eye to their presence. When top leadership has been detained, they have been kept as bargaining chips instead of being extradited.

In 2009, Pakistan sent troops into the Swat Valley in a bid to retake control from Taliban-allied militants there. Within months, it claimed victory, but the militants’ leadership, including the group’s head Maulana Fazlullah, had escaped, making their way through Dir and across the border to Kunar.

When a drone strike killed the TTP’s head, Hakimullah Mehsud, this November, Fazlullah took his place. He has since made several trips to Pakistan, attending TTP meetings in North Waziristan, but is thought to still have safe-houses in Kunar.

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Pakistan, which would like to negotiate a peace deal with the TTP, needs to get access to Fazlullah, but the key middle man is sitting in an NDS prison in Afghanistan.

Maulvi Faqir Muhammad was one of the founding members of the TTP, and commanded a force of more than six thousand fighters – Pakistanis, Afghans, and Arabs – in his native Bajaur Agency. When Pakistani troops flushed militants out of Bajaur in 2010, Faqir moved across the border into Afghanistan.

Faqir had a falling out with TTP leadership last year, when he openly called for negotiations with the Pakistani government. But he was reinstated soon after, at the behest of Fazlullah, and it is thought Faqir could help persuade the TTP head to consider peace talks. Or, if things don’t work out, Faqir could help locate Fazlullah so Pakistan, or maybe a U.S. drone strike, could take him out.


Getting to Fazlullah means getting at Faqir, much like finding Hakimullah Mehsud needed the cooperation of Latif Mehsud, who reportedly provided the intelligence used to locate the TTP’s former leader.

This February, Faqir was arrested by Afghan intelligence agents, and Karzai’s government has refused to extradite him to Pakistan. Afghan officials have said they are unwilling to do so until Pakistan hands over senior Taliban leaders in its custody like Mullah Baradar. Baradar was once the second in command of the Afghan Taliban, and is the natural point of contact for initiating peace talks between the insurgents and the Afghan government. Pakistan released him from prison in September, but only recently allowed Afghan negotiators limited access to him.

So each country now controls access to key militant leaders that could be used to influence the insurgency plaguing its rival.

Even as the covert war between Afghanistan and Pakistan continues, real skirmishes at the border have seen a dramatic rise over the last few years, foreshadowing the kind of tensions that might arise after coalition forces withdraw.

Pakistan and Afghanistan maintain more than a thousand border posts along the disputed, largely unmarked 2,600 kilometer border, but militants still move across with apparently little difficulty.

Pakistani forces have been known to, at the very least, ignore Haqqani network militants launching attacks into Afghanistan, but officials have also long accused the Afghans of doing the same thing.

In 2010, U.S. troops pulled out of strategic areas along the border like the Korengal Valley, redeploying to urban centers to protect the population from the Taliban insurgency. The move left a hole in the border, allowing for militants based in Kunar to strike targets in Pakistan.

In August, 2011, more than three hundred TTP fighters – Afghans and Pakistanis – crossed the border into Pakistan’s Chitral region, carrying out assaults on seven security posts over the course of several days, killing 32 Pakistani security personnel.

Two months later, more than two hundred fighters crossed into Pakistan’s Upper Dir area, sparking clashes that left one Pakistani soldier and 30 militants dead.

In neighboring Bajaur Agency, which Pakistan says it had cleared of militants by 2010, groups of up to 300 militants crossed over from Afghanistan during the summer of 2011 on three separate occasions, attacking government security posts and sparking clashes that lasted several days.

The raids have continued unabated in the last two years. In an effort to pursue the fighters, Pakistan routinely shells Afghanistan, often drawing retaliatory shelling by the Afghan National Army, which also fires at insurgents fleeing its own forces. Between the raids and the shelling, there has been a dramatic rise in casualties in the region: in 2009, 15 people were killed in cross-border violence, by 2012 the number of dead had reached 314.

If U.S. troops leave a vacuum in Afghanistan that the Haqqani insurgents begin to exploit, the Afghans are going to want leverage to force Pakistan to crack down on sanctuaries in its territory, and it seems that leverage will be the TTP. If the TTP’s insurgency in Pakistan picks up and the group’s leadership is still operating out of Afghanistan, there will be intense pressure on the Pakistanis to take military action – perhaps even a ground incursion – across the border.


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Unless the Taliban on both sides of the border are pacified – either politically or militarily – before the U.S. withdrawal, the cross-border skirmishes could turn into an all-out war.

Umar Farooq is based in Pakistan, where he works as a correspondent for the Christian Science Monitor and the Wall Street Journal. He has also written for The Atlantic, Foreign Policy, The Globe and Mail, and The Nation.