Jacquelyn Martin / AP
Secretary of State John Kerry shakes hands with Afghan President Hamid Karzai after a press conference at the Presidential Palace in Kabul on Saturday.
Secretary of State John Kerry, who is on an unannounced trip to Afghanistan, has delayed his departure from Kabul by several hours as negotiations about a security agreement with President Hamid Karzai drag on, while the U.S. detention of a top Pakistani Taliban commander has also soured the mood for discussions about the future role of U.S. troops in the country.
The focus of Kerry's unscheduled trip to Afghanistan has been the Bilateral Security Agreement - which will sketch out the proposed U.S. military presence in Afghanistan after the 2014 withdrawal. The deadline for finalizing the agreement looms at the end of October.
Hours into the delay, a senior State Department official told NBC News that, "Secretary Kerry sees an opening to continue making headway on issues including security and sovereignty this evening and wants to leave Kabul with as many issues resolved as possible to set up conditions for finalizing an agreement."
The BSA has been under negotiation for a year, and could potentially keep as many as 10,000 U.S. troops deployed on Afghan soil after 2014.
But as the U.N. Security Council voted on Oct. 11 for an extension of NATO/ISAF presence in Afghanistan, confirming US military presence here until Dec. 31 of next year, the potential agreement between Kabul and Washington is stuck on two points: how much authority and autonomy will U.S. troops have as they stay on in Afghanistan, and whether the U.S. will officially underwrite itself to come to Afghanistan's defense if the latter is attacked. Sources in the Karzai administration say that the U.S. is more interested in "extra leverage" regarding American troop presence, while the Afghan government wants to seal the defense clause. As the talks entered a third round late Saturday, an Afghan official briefed reporters that the issue of preventing civilian casualties by NATO personnel is also under discussion.
Meanwhile, the detention of a top Pakistani Taliban commander by U.S. forces -- who apprehended Latif Mehsud, 35, the deputy emir of the Tahrik-e-Taliban Pakistan [the Movement of Taliban in Pakistan, or TTP] -- has "enraged" President Karzai, according to sources in the Afghan administration.
Mehsud was traveling with officers of the Afghan intelligence service, the NDS, when his convoy was intercepted and he was apprehended by US forces.The Pakistani Taliban said he was captured in the Khost province while security officials said he held in Logar province.
Senior Pakistani Taliban leaders have also confirmed to NBC News that Mehsud is missing and that they "are surprised why he was meeting Afghan intelligence officials."
Mehsud is the operations chief of the TTP, which is essentially at war with the Pakistani state, but has also engaged U.S. forces in Afghanistan. Not directly involved with the Afghan Taliban, the TTP is based in North and South Waziristan - the sites of most of the drone attacks that target Pakistan's tribal areas - from where it has attacked mainland Pakistan as well as struck against US targets across the border. The TTP has claimed responsibility for the 2009 suicide bombing of Camp Chapman in Afghanistan, which killed seven CIA officers, and an attempted car bombing in New York City's Times Square in 2010.
Mehsud has served as both the bodyguard and personal driver of Hakimullah Mehsud, the charismatic chief of the Pakistani Taliban.
He was coordinating the broad operations of the Pakistani Taliban, in charge of appointments of office-holders and commanders in the TTP's structure and was also involved in backdoor talks with the Pakistani government.
Taliban officials assessed, under the condition of anonymity, that Mehsud may have been negotiating the release of Afghan soldiers with the NDS when he was captured by American forces, while a Pakistani security official told NBC News that Mehsud may have gone for a "meet and greet" with Afghan intelligence officials.
Mehsud's is one of the highest-profile arrests ever made by U.S. forces from the ranks of the larger Taliban militancy movement. This week saw the U.S. enter the 13th year of its military operations in Afghanistan.
"He was so close to Hakimullah Mehsud and that's why he made him his deputy," a senior Taliban leader said.
Pleading anonymity, he said Said Khan, alias Commander Sajna, was earlier made the deputy chief of the TTP when Maulana Waliur Rahman was killed in drone attack on May 29 this year in Miranshah, North Waziristan. However, Commander Sajna, considered in favour of peace talks with Pakistan government, developed differences with Hakimullah Mehsud and thus he replaced him with Latif Mehsud.
Pakistani officials said Latif Mehsud was against peace talks between Pakistan the Taliban groups.
NBC News' Mushtaq Yusufzai contributed to this report.
First published October 12 2013, 10:02 AM