Mullah Abdul Salam Zaaef, former Taliban ambassador in Pakistan, former Guantanamo detainee, and adviser on reconciliation to President Karzai, told the New York Times this week that Mullah Baradar's arrest could be disastrous. "If it is really true, it could seriously affect negotiations, and gravely affect the peace process," he said in Kabul. And that may be just what the old hardliners of the ISI want.

From the NYT

ISLAMABAD, Pakistan — Inside a secret detention center in an industrial pocket of the Pakistani capital called I/9, teams of Pakistani and American spies have kept a watchful eye on a senior Taliban leader captured last month. With the other eye, they watch each other.

The C.I.A. and its Pakistani counterpart, the Directorate of Inter-Services Intelligence, have a long and often tormented relationship. And even now, they are moving warily toward conflicting goals, with each maneuvering to protect its influence after the shooting stops in Afghanistan.

Yet interviews in recent days show how they are working together on tactical operations, and how far the C.I.A. has extended its extraordinary secret war beyond the mountainous tribal belt and deep into Pakistan’s sprawling cities.

Beyond the capture of Mullah Abdul Ghani Baradar, C.I.A. operatives working with the ISI have carried out dozens of raids throughout Pakistan over the past year, working from bases in the cities of Quetta, Peshawar and elsewhere, according to Pakistani security officials.

The raids often come after electronic intercepts by American spy satellites, or tips from Pakistani informants — and the spies from the two countries then sometimes drive in the same car to pick up their quarry. Sometimes the teams go on lengthy reconnaissance missions, with the ISI operatives packing sunscreen and neon glow sticks that allow them to identify their positions at night.

Successful missions sometimes end with American and Pakistani spies toasting one another with Johnnie Walker Blue Label whisky, a gift from the C.I.A.

The C.I.A.’s drone campaign in Pakistan is well known, which is striking given that this is a covert war. But these on-the-ground activities have been shrouded in secrecy because the Pakistani government has feared the public backlash against the close relationship with the Americans.

In strengthening ties to the ISI, the C.I.A. is aligning itself with a shadowy institution that meddles in domestic politics and has a history of ties to violent militant groups in the region. A C.I.A. spokesman declined to comment for this article.

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The UN's former envoy to Afghanistan, Kai Eide, has strongly criticised Pakistan's recent arrest of high-ranking Taliban leaders.

Mr Eide told the BBC the arrests had completely stopped a channel of secret communications with the UN.

Pakistani officials insist the arrests were not an attempt to spoil talks.

Mr Eide confirmed publicly for the first time that his secret contacts with senior Taliban members had begun a year ago.

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