ISLAMABAD, Pakistan — When American and Pakistani agents captured Abdul Ghani Baradar, the Taliban’s operational commander, in the chaotic port city of Karachi last January, both countries hailed the arrest as a breakthrough in their often difficult partnership in fighting terrorism.
But the arrest of Mr. Baradar, the second-ranking Taliban leader after Mullah Muhammad Omar, came with a beguiling twist: both American and Pakistani officials claimed that Mr. Baradar’s capture had been a lucky break. It was only days later, the officials said, that they finally figured out who they had.
Now, seven months later, Pakistani officials are telling a very different story. They say they set out to capture Mr. Baradar, and used the C.I.A. to help them do it, because they wanted to shut down secret peace talks that Mr. Baradar had been conducting with the Afghan government that excluded Pakistan, the Taliban’s longtime backer.
In the weeks after Mr. Baradar’s capture, Pakistani security officials detained as many as 23 Taliban leaders, many of whom had been enjoying the protection of the Pakistani government for years. The talks came to an end.
The events surrounding Mr. Baradar’s arrest have been the subject of debate inside military and intelligence circles for months. Some details are still murky — and others vigorously denied by some American intelligence officials in Washington. But the account offered in Islamabad highlights Pakistan’s policy in Afghanistan: retaining decisive influence over the Taliban, thwarting archenemy India, and putting Pakistan in a position to shape Afghanistan’s postwar political order.
“We picked up Baradar and the others because they were trying to make a deal without us,” said a Pakistani security official, who, like numerous people interviewed about the operation, spoke anonymously because of the delicacy of relations between Pakistan, Afghanistan and the United States. “We protect the Taliban. They are dependent on us. We are not going to allow them to make a deal with Karzai and the Indians.”
Some American officials still insist that Pakistan-American cooperation is improving, and deny a central Pakistani role in Mr. Baradar’s arrest. They say the Pakistanis may now be trying to rewrite history to make themselves appear more influential. It was American intellgence that led to Mr. Baradar's capture, an American official said.
“These are self-serving fairy tales,” the official said. “The people involved in the operation on the ground didn’t know exactly who would be there when they themselves arrived. But it certainly became clear, to Pakistanis and Americans alike, who we’d gotten.”
Other American officials suspect the C.I.A. may have been unwittingly used by the Pakistanis for the larger aims of slowing the pace of any peace talks.
At a minimum, the arrest of Mr. Baradar offers a glimpse of the multilayered challenges the United States faces as it tries to prevail in Afghanistan. It is battling a resilient insurgency, supporting a weak central government and trying to manage Pakistan’s leaders, who simultaneously support the Taliban and accept billions in American aid.
A senior NATO officer in Kabul said that in arresting Mr. Baradar and the other Taliban leaders, the Pakistanis may have been trying to buy time to see if President Obama’s strategy begins to prevail. If it does, the Pakistanis may eventually decide to let the Taliban make a deal. But if the Americans fail — and if they begin to pull out — then the Pakistanis may decide to retain the Taliban as their allies.
“We have been played before,” a senior NATO official said. “That the Pakistanis picked up Baradar to control the tempo of the negotiations is absolutely plausible.”
As for Mr. Baradar, he is now living comfortably in a safe house of Pakistan’s intelligence agency, the Pakistani official said. “He’s relaxing,” the official said.
Many of the other Taliban leaders, after receiving lectures against freelancing peace deals, have been released to fight again.
Exactly why the Pakistan’s intelligence agency, the Directorate for Inter-Services Intelligence, or ISI, became so alarmed at the Afghan peace talks is unclear. In retrospect, paranoia seems to have figured as much as national self-interest.
A senior Afghan official said that beginning late last year, his government had reached out to a number of Taliban leaders to explore the prospect of a deal. Among them were Mr. Baradar and another Taliban leader named Tayyib Agha. The Afghan official declined to say who met the Taliban leaders, but reports of such meetings have since surfaced. Ahmed Wali Karzai, the president’s brother, reportedly met Mr. Baradar in January, according to a former Afghan official and a former NATO official. Mr. Karzai’s brother denies it.
In another overture, Engineer Ibrahim, then the deputy chief of the Afghan intelligence service, met with a group of Taliban leaders in Dubai, according to a prominent Afghan with knowledge of the meeting. Mr. Ibrahim, now with the National Security Council, could not be reached for comment on Sunday.
A Pakistani spiritual leader close to the Taliban leadership said that, earlier this year, he had received a message through an intermediary that Mr. Karzai wanted to talk peace. “We rejected it,” he said.
The discussions with Mr. Baradar and the other Taliban were in their early phases, but they seemed promising, the Afghan official said. Their aim was to establish conditions under which formal talks could begin.
“It was the beginning of a negotiation, so both sides staked out extreme positions,” the Afghan official said. “But we sensed a readiness for peace.”
When Pakistani intelligence officials learned of the overtures, they became unnerved by what they saw as an attempt by the Afghans to strike a peace deal without them. In particular, the ISI suspected the Americans were orchestrating the talks.
In January, days before Mr. Baradar’s capture, a senior ISI official told The New York Times that his agency was hunting the Taliban leader because he was in contact with the Americans. The ISI official accused the Americans of disregarding Pakistan’s legitimate security interests.
“We are after Mullah Baradar,” the senior ISI official said. “We strongly believe the Americans are in touch with him.”
A second ISI official confirmed that the Pakistanis had decided to go after Mr. Baradar to shut down what they feared were blossoming peace talks.
“This is a national secret,” he said. “The Americans and the British were going behind our backs, and we couldn’t allow that.” American and British officials denied they were directly involved in talks with the Taliban.
Once the decision was made to detain Mr. Baradar, the Taliban leader was tracked to Karachi, a sprawling, violent city of nearly 20 million people. There, the Pakistani official said, ISI agents waited for him to activate his cellphone. After several days, the alarm went off, and the agency narrowed Mr. Baradar’s whereabouts to a densely populated area of about two square miles.
That was as far as the intelligence agency’s technology would go, the Pakistani official said. To pinpoint Mr. Baradar’s location, ISI agents turned to the C.I.A.
Since 2001, the C.I.A. and the ISI have maintained an uneasy relationship. They have cooperated on hundreds of operations and detained dozens of militants, but they have clashed over the ISI’s support for the Taliban.
Within minutes of Mr. Baradar’s cellphone activation, the C.I.A. sent two unarmed American technicians to join the Pakistani intelligence agency’s team, the Pakistani official said.
Activating a portable tracking device, the C.I.A. team quickly led the ISI to Mr. Baradar’s home. Only four hours after his cellphone went on, Mr. Baradar was in Pakistani custody, the Pakistani official said. According to the Pakistani official, the ISI did not inform the Americans of the identity of the target.
American officials disputed this account, saying the intelligence indicated that the target was related to Mr. Baradar. But they conceded that they did not know the identity of Mr. Baradar until after the arrest.
The Pakistanis refused to allow the C.I.A. to interrogate Mr. Baradar or even to be present when they spoke. Another Pakistani official said Mr. Baradar was taken to a safe house in Islamabad, where he was debriefed. It was only several days later that the C.I.A. learned of his identity and were allowed to question him.
The Pakistani official even joked about the C.I.A.’s naïveté. “They are so innocent,” he said.
Some American officials insist that while the C.I.A. may not have known whom the Pakistanis were capturing, the Pakistanis did not know either. They speculated that once the Pakistanis had Mr. Baradar, they may have decided to hold him to scuttle the peace talks. It was then, some American officials say, that the Pakistanis may have decided to detain the other Taliban leaders.
“We are not convinced that that was why Baradar was picked up,” an American official in the region said, referring to the Afghan talks. “But maybe that was why he was held.”
Yet other American officials said the Pakistani version seemed more credible than the C.I.A.’s. “Baradar is too high-profile for them not to have known who it was,” the senior NATO official said.
Within days of Mr. Baradar’s arrest, Pakistani agents picked up as many as 22 other Taliban leaders across Pakistan, according to an official with the United Nations in Kabul. The detentions included some of the most senior Taliban commanders, including Mullah Qayoom Zakir, Abdul Kabeer and Abdul Rauf Khadem.
“We know where the shadow government is,” the Pakistani security official said.
The official said the detained Taliban leaders were warned against carrying out future negotiations without their permission. A former Western diplomat, with long experience in the region, confirmed that the ISI sent a warning to its Taliban protégés.
“The message from the ISI was: no flirting,” he said.
Afghans close to the Taliban said the arrests of Mr. Baradar and the others illustrated the strained relationship between the Taliban and their benefactors in Pakistani intelligence. The ISI may protect the Taliban’s leaders, they said, but they also limit their freedom. “When we try to act on our own, they stop us,” the Pakistani spiritual leader said.
Since then, many of the Taliban leaders who were detained have been set free, officials said. Principal among them is Mr. Zakir, a Taliban commander who was released from the American prison at Guantánamo Bay in 2006.
Mr. Zakir, who took over for Mr. Baradar, is regarded as more brutal than his predecessor, unconcerned about civilian casualties — and less inclined to do a deal with the Karzai government.