Pakistan’s Inter-Services Intelligence (ISI) chief Lt. Gen. Ahmad Pasha is reported in one plot to have visited a number of Arab countries to discuss their potential support for a military coup against President Asif Ali Zardari, accusing Zardari of undermining the nation’s sovereignty.

Meanwhile, Zardari’s own plot against the military, the “coup memo” sent to US military commander Admiral Michael Mullen seeking his support in removing the Pakistani military leadership by force, has taken on a more serious tone with Army Chief of Staff General Parvez Kayani reporting that the military has found the memo to be authentic.

Kayani says the military came to this conclusion during a meeting with President Zardari, himself, Lt. Gen. Pasha, and former Pakistani Ambassador to the United States Husain Haqqani, saying that the evidence was strong that the memo was authentic. Lt. Gen. Pasha offered a four page statement as well saying he was convinced that the memo, delivered by Pakistani-American businessman Mansour Ijaz was real.

The ruling Pakistani Peoples Party (PPP) has repeatedly denied that the memo was real, but now seems to be taking an alternate tack, claiming the Supreme Court lacks jurisdiction in inquiry into a possible coup by the civilian government.

Opposition politicians who had already called for Zardari’s ouster over the coup memo now find themselves adding to that a call for Lt. Gen. Pasha to resign over his possible exploration of a coup on his own. Pakistan has a long history of coups, but with popular support for both he military and the Zardari government at relative lows, it may be difficult for either to consolidate power even if they decide to push their rival out of the way.

Panetta arrived in Pakistan on Friday and immediately accused the Zardari government of harboring elements that are secretly colluding with militants. Defense Secretary Robert Gates continued this theme today, expressing regret over sharing information with the country.

As with several other high profile Pakistan visits, Panetta’s was ostensibly aimed at improving ties with the nation, with an undercurrent of issuing new demands to the nation’s military. Officials said Panetta was surprisied at the “rigidity” of Pakistan’s army chief Gen. Parvez Kayani.

But perhaps he oughtn’t be. Each recent visit by officials has ended exactly the same way, with officials issuing demands, making accusations, and departing with relations even worse than they were before. In that respect Panetta’s visit was more of the same.

So when he turned up missing this weekend, his family assumed he had been picked up by the ISI for a report about terrorist infiltration of Pakistan’s Navy, which came in the wake of the Karachi attack. They also assumed it was another warning, and he’d eventually be released unharmed.

But this time, Shahzad was found dead in his car, near the capital city of Islamabad. He was 100 miles from his home, and his body showed signs of a savage beating. It is widely assumed this was the ISI’s handiwork as well.

Of course the ISI has condemned the notion, saying it was “totally absurd” to suggest that the nation’s secretive military spy agency would be responsible for the killing. Still, the death will only add more uncomfortable attention to the shadowy agency, and will fuel distrust of its motives.

That is because among those reasons is “association with Pakistan ISID,” the Inter-Services Intelligence agency, which is the Pakistani government’s top spy agency. In addition to the agency’s significant influence, the current army Chief of Staff Gen. Parvez Kayani also was the former ISI chief.

The document didn’t stop there, either. Near the end, the file lists “associated forces” of al-Qaeda, and again lists the Pakistan ISI as having “an established working, supportive or beneficiary relationship for the achievement of common goals.”

The leak comes less than a week after Admiral Michael Mullen accused “some” elements of the ISI of having terror ties. The document appears to take this much further and treats the agency in general as a terrorist auxiliary for al-Qaeda.

This has spawned further concerns that the leaks will make the already tense US-Pakistan relationship even worse. The Pakistani government has been railing at the US for drone strikes and CIA operations for weeks, but the Obama Administration appears to have largely ignored the demands and continued with business as usual.

The summons deals with a lawsuit filed last month in Brooklyn Federal Court accusing the Pakistani government in general and the ISI in particular of “complicity” in the November 2008 attacks in Mumbai. The lawsuit was brought by relatives of two of the victims.

In addition to the ISI and the government, the banned Lashkar-e Taiba (LeT) organization was also named in the suit. LeT has been accused of being behind the attack though the organization has denied any direct involvement.

The lawsuit is expected to generate considerable publicity against Pakistan at a time when the Obama Administration is said to be mulling a ground invasion of northern Pakistan. It seems unlikely, however, that enough evidence can be brought to bear to prove ISI involvement in the attack.

Officials say that there are as many as 20 British citizens in North Waziristan and “several dozen” people with citizenship elsewhere in Europe. Militant groups have been keen to recruit people with such citizenship because they could travel freely within the European Union.

The report may well be linked to last week’s claims of a “credible but non-specific” plot to carry out a Mumbai-style attack against some site in Europe or North America. The US has insisted that the massive escalation of drone strikes into the tribal areas is because of the plot.

Yet ironically it is opposition to those drone strikes and to the US-led war in Central Asia in general which is fueling the surprising trend of educated, not-particularly-religious Western citizens seeking to carry out militant attacks across the West.

The most obvious previous example would be the Times Square bomber, who started out as a relatively anonymous financial advisor living in Connecticut before deciding to travel to Pakistan to seek training and carry out his (ultimately failed) attack. Increasing concern about people who aren’t exactly “likely suspects” is fueling a flurry of new warnings about the attacks, and a US travel advisory against the entire continent of Europe.

Perhaps the most fascinating part of this is that the threat seems to be the first fallout from the WikiLeaks release of some 92,000 Afghan War related US documents.

Yet these documents were all between 1-6 years old, and while the leak was new the public it cannot have possibly been new for the Obama Adminstration. Officials must surely have been aware of all of this evidence over the past weeks, as they arrived in Pakistan to pledge large increases in aid.

Afghan officials for their part condemned Pakistan, though the ISI itself angrily shot back that the US allegations were “mostly from Afghan intelligence, so you can imagine their credibility.” The US documents detail a number of alleged ISI plots, including a claimed plot to poison all the beer in Afghanistan to kill Western troops.

Reports from the Associated Press say that the CIA has issued private complaints to the Pakistani government about an apparent attempt by the ISI to plant a “double agent” in the American spy agency.

Reportedly, the CIA was approached by a Pakistani man claiming to have information about Pakistan’s nuclear weapons program, and who came with spent fuel rods from the program. After probing, the CIA decided the man was sent by ISI specifically to infiltrate the CIA and provide data on American spying inside Pakistan. Pakistan promised to “look into” the matter but it appears nothing ever came of it.

The US relation toward the ISI is somewhat bizarre. While officials have endlessly claimed the ISI is providing “direct support” for the Taliban, the CIA is also direct funding the agency, providing upwards of a third of the ISI’s operating budget annually.

Baradar was arrested last month in Karachi after a US tip, and Interior Minister Rehman Malik initially indicated that he would be extradited to Afghanistan as soon as they requested him. Repeated requests, however, have led to a messy court battle in Pakistan and an increasingly reluctant government.

Reportedly Pakistani officials are concerned that if they hand Baradar over to Afghanistan he will wind up in US custody in short order and will disappear into a CIA interrogation center somewhere.

But the fight over the mullah actually goes much deeper than that. Afghan President Hamid Karzai was reportedly in direct talks with Baradar over a possible reconciliation jirga before his arrest. As one of the more moderate Taliban leaders, Baradar penned a guide urging militants to avoid killing civilians, and was seen as a promising peace partner.

But the Pakistani government was basically obliged to arrest him after the US “tipoff,” and their Inter-Services Intelligence (ISI) agency is reportedly irked that Baradar was talking to Afghanistan directly. Pakistan has long sought to use the ISI’s traditional links with the Taliban to fascilitate peace talks, and was apparently none too happy at being cut out of the deal. Karzai was reportedly angry with the arrest, which will likely do serious harm to the jirga.

Security officials say Baradar is being held by the Inter-Services Intelligence (ISI) agency, at their Karachi directorate. They say he has provided “useful information” to Pakistan, who has passed it along to the US.

Baradar is said to be in charge of military operations for the Taliban in southwestern Afghanistan, and some suggest he may in fact be the organization’s de facto second in command.

Though some have expressed hope that this capture would be of enormous significance, it is hardly without precedent. In 2007 the Taliban’s previous second-in-command, former Defense Minister Mullah Obaidullah, was
captured in Pakistan as well. Obaidullah’s current status is unknown, the Taliban claims they recovered him in a “prisoner swap” for Pakistani Ambassador to Afghanistan Tariq Azizuddin. Pakistan denied the swap but hasn’t commented on where Obaidullah currently is.