In the New York Times, Dexter Filkins reports:

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.”

My question: Did the New York Times really need six months to piece this story together?

Back on February 17, I wrote a post headlined: “Was the arrest of the Taliban’s second-in-command a strategic blunder?” This is what I wrote:

The capture of the Taliban’s second in command, Mullah Abdul Ghani Baradar, has been hailed as a huge blow to the Taliban but it may turn out to deliver an even bigger blow to President Obama’s hopes for an early withdrawal of US troops from Afghanistan.

Hajji Agha Lalai, former head of the Afghan government-led reconciliation process in Kandahar, who has dealt with members of the Taliban leadership council for several years, said Mullah Baradar was “the only person intent on or willing for peace negotiations.”

Last month Baradar facilitated an inconclusive meeting in Dubai between midlevel Taliban commanders and Kai Eide, the departing top UN official in Kabul, according to McClatchy newspapers.

Saeed Shah reported:

According to Vahid Mojdeh, a former Afghan official who worked under the Taliban, Baradar was instrumental in reining in insurgent violence, by banning sectarian killings and indiscriminate bombings.

“Baradar was an obstacle against al-Qaida, who wanted to make an operation in Afghanistan like they did in Iraq,” Mojdeh said. “But Baradar would not allow them to kill Shias” – the minority Muslim sect – “or set off explosions in crowded places.”

Pakistani analysts said Baradar’s capture suggested either that Islamabad had abandoned its attempt to promote peace talks or the Taliban number two had fallen afoul of the Pakistani authorities. Analysts said Baradar was the most likely point of contact for any future talks.

“This is inexplicable. Pakistan has destroyed its own credentials as a mediator between Taliban and Americans. And the trust that might have existed between Taliban and Pakistan is shattered completely,” said Rustam Shah Mohmand, a former Pakistani ambassador to Kabul after the overthrow of the Taliban.

The capture of Mullah Baradar has been widely reported as the result of a coordinated operation between the US and Pakistan, but so far the story seems very murky.

On Tuesday, February 9, the New York Times reported:

Pakistan has told the United States it wants a central role in resolving the Afghan war and has offered to mediate with Taliban factions who use its territory and have long served as its allies, American and Pakistani officials said.

The offer, aimed at preserving Pakistan’s influence in Afghanistan once the Americans leave, could both help and hurt American interests as Washington debates reconciling with the Taliban.

Pakistan’s army chief, Gen. Ashfaq Parvez Kayani, made clear Pakistan’s willingness to mediate at a meeting late last month at NATO headquarters with top American military officials, a senior American military official familiar with the meeting said.

The report said that General Kayani rebuffed US pressure to expand operations against the Taliban in North Waziristan because “the Pakistani Army still regarded India as its primary enemy and was stretched too thin to open a new front.”

Within days we learn of Mullah Baradar’s arrest in Karachi, Pakistan. His capture could cripple the Taliban’s military operations, at least in the short term, says Bruce Riedel, an adviser to the Obama administration. Others in Washington describe this as a huge blow to the Taliban.

But the New York Times now reports:

The arrest followed weeks of signals by Pakistan’s military chief, Gen. Ashfaq Parvez Kayani — to NATO officials, Western journalists and military analysts — that Pakistan wanted to be included in any attempts to mediate with the Taliban.

Even before the arrest of the Taliban commander, Mullah Abdul Ghani Baradar, a senior Pakistani intelligence official expressed irritation that Pakistan had been excluded from what he described as American and Afghan approaches to the Taliban.

“On the one hand, the Americans don’t want us to negotiate directly with the Taliban, but then we hear that they are doing it themselves without telling us,” the official said in an interview. “You don’t treat your partners like this.”

Mullah Baradar had been a important contact for the Afghans for years, Afghan officials said. But Obama administration officials denied that they had made any contact with him.

Whatever the case, with the arrest of Mullah Baradar, Pakistan has effectively isolated a key link to the Taliban leadership, making itself the main channel instead.

While Washington denied prior negotiations with Baradar, a US intelligence official in Europe claimed otherwise:

“I know that our people had been in touch with people around him and were negotiating with him,” the official said, speaking on the condition of anonymity because he was not authorized to discuss the issue.

“So it doesn’t make sense why we bite the hand that is feeding us,” the official added. “And now the Taliban will have no reason to negotiate with us; they will not believe anything we will offer or say.”

Update (2/17/10): In an interview on NPR Ahmed Rashid speculated that now that Baradar is in custody he could be in a better position to negotiate. Why? Because he’s not going anywhere?

Much more plausible is that the Pakistanis pulled him in — Rashid acknowledges that Baradar’s whereabouts have never been unknown to the ISI — because they didn’t want to be cut out of the negotiating loop by Americans negotiating directly with the Taliban. In other words, Pakistan is not willing to see a deal agreed to end this war without being able to dictate some of the terms.

If that is the case, no wonder The White House asked its news outlet (the New York Times) to sit on the story for a few days while they decided how it should be told.