The Inter-Services Intelligence Directorate, or ISI, is commonly seen by Pakistanis and foreigners alike as the most powerful institution in the Pakistani government. Pakistan’s civilian politicians are often wobbly on core issues that concern the United States and the international community. Most of the bureaucrats in the ministries, as well as most of the city level officials, are seen as corrupt players in a duplicitous Pakistani political atmosphere.

The Pakistani military and its partners at the ISI, on the other hand, are often the first that are met by American diplomats when they travel to the country. The ISI is responsible for the one policy area that the Pakistani government is incessantly focused on — self preservation. Intelligence officials in the directorate are both feared and loved in Pakistan. Feared because the organization lurks in the shadows and is known for making dissidents disappear but loved because Pakistani intelligence chiefs are the first line of defense against their Indian archival.

Indeed, the United States fully grasps the civil-military power imbalance in Pakistan. Prime ministers like Benazir Bhutto and Yousaf Raza Gilani and presidents like Asif Zardari and Nawaz Sharif are no match for the likes of a Pervez Musharraf, Parvez Kayani and Ahmed Shuja Pasha. Pakistani politicians have even expressed their deep displeasure with the army meddling in civilian politics — an intervention that sometimes overturns everything these men and women have been working for throughout their careers.

Nevertheless, the army is still what draws the American foreign policy establishment into the country on most of the important issues. The conventional wisdom is that the United States can always worry about Pakistan’s economy at a later date. It is Afghanistan, terrorism, Islamist extremism, nuclear proliferation and South Asian security that need to be dealt with now.

Yet the ISI, and indeed the Pakistani Military as a whole, has had a particularly bad month. After failing to detect American aircraft during the Osama bin Laden operation, Pakistani generals were lambasted by their civilian counterparts for incompetence. It did not help the military’s case that the world’s most wanted terrorist was hiding out only a few miles from Pakistan’s equivalent of West Point.

Then, weeks later, militants associated with the Tehrik i-Taliban Pakistan (or Pakistani Taliban) launched a highly coordinated and impressive strike against a Pakistani naval base in the port city of Karachi. The insurgent group held the base for roughly fifteen hours until they were driven out and killed by security forces. The episode claimed the lives of ten security personnel and the destruction of two American-made planes. The attack once again highlighted worries over whether the lower levels of Pakistan’s armed forces were being infiltrated by extremists, a concern that American officials have been carrying for years.

But the latest incident — the abduction and killing of a Pakistani journalist — will perhaps receive the most attention and the most criticism from members of Pakistan’s press and civilian government. While the ISI has not been fingered for the journalist’s death, human rights groups suspect that the intelligence organization may have been involved.

The ISI is the lead spy agency against other countries but the organization is also known for monitoring its own citizens. It is almost routine procedure for Pakistani journalists to be rounded up by Pakistani intelligence over reporting that the agency deems unflattering. The military brass looks down upon any article, story or television program that spurs a negative reaction toward the security establishment, often calling such articles schemes meant to deliberately weaken their support and institutional prestige among Pakistani society. Umar Cheema, an award winning investigative journalist, was kidnapped and beaten last year for an article that he had written about the army. The ISI was never implicated for the beating, but Mr Cheema believes that they were the ones who carried out the abduction.

The death of Syed Saleem Shahzad on May 31 may be another case of journalism being punished by the Pakistani state. Kidnapped in Islamabad, he was found dead one hundred and fifty miles away from the capital, his bloated body showing marks of beatings and torture. The ISI quickly denied accusations that it was involved but its leadership certainly had a motive — Shahzad’s latest piece was about a possible connection between Islamic militants and the Pakistani army. Shahzad also reported to Human Rights Watch, the most internationally respected human rights watchdog group, that he was receiving threats from the ISI for years over his work.

The Committee to Protect Journalists already ranks Pakistan as the most dangerous place for reporters. The disappearance and killing of another, whoever was involved, will not help the country move down the list. And neither will the ISI regain its international credibility if instances like this continue to occur. In world politics, you do not need to be proven guilty. Mere speculation is often enough to warrant a guilty verdict. In this case, there is plenty of suspicion to go around for Pakistan’s intelligence directorate.