Declan Walsh reports:

A prominent Pakistani journalist who investigated links between the military and al-Qaida has been found dead, triggering angry accusations against the powerful Inter-Services Intelligence spy agency.

Saleem Shahzad, Pakistan correspondent for a news service based in Hong Kong, disappeared on his way to a television interview in Islamabad on Sunday evening. On Tuesday, police said they found his body on a canal bank in Mandi Bahauddin, 80 miles south-east of the capital.

Shahzad’s abandoned car was found 25 miles away. Television images of his body showed heavy bruising to his face. Media reports said he had a serious trauma wound to the stomach.

Human Rights Watch had already raised the alarm over the disappearance of the 40-year-old father of three, citing a “reliable interlocutor” who said he had been abducted by ISI.

“This killing bears all the hallmarks of previous killings perpetrated by Pakistani intelligence agencies,” said a senior researcher for Human Rights Watch in south Asia, Ali Dayan Hasan. He called for a “transparent investigation and court proceedings”.

Other journalists reacted angrily, directly accusing ISI of responsibility on television and social media. “Any journalist here who doesn’t believe that it’s our intelligence agencies?” tweeted Mohammed Hanif, a bestselling author.

In his last published report, Shahzad wrote:

Al-Qaeda carried out the brazen attack on PNS Mehran naval air station in Karachi on May 22 after talks failed between the navy and al-Qaeda over the release of naval officials arrested on suspicion of al-Qaeda links, an Asia Times Online investigation reveals.

Pakistani security forces battled for 15 hours to clear the naval base after it had been stormed by a handful of well-armed militants.

At least 10 people were killed and two United States-made P3-C Orion surveillance and anti-submarine aircraft worth US$36 million each were destroyed before some of the attackers escaped through a cordon of thousands of armed forces.

An official statement placed the number of militants at six, with four killed and two escaping. Unofficial sources, though, claim there were 10 militants with six getting free. Asia Times Online contacts confirm that the attackers were from Ilyas Kashmiri’s 313 Brigade, the operational arm of al-Qaeda.

Three attacks on navy buses in which at least nine people were killed last month were warning shots for navy officials to accept al-Qaeda’s demands over the detained suspects.

The May 2 killing in Pakistan of Osama bin Laden spurred al-Qaeda groups into developing a consensus for the attack in Karachi, in part as revenge for the death of their leader and also to deal a blow to Pakistan’s surveillance capacity against the Indian navy.

The deeper underlying motive, though, was a reaction to massive internal crackdowns on al-Qaeda affiliates within the navy.

Several weeks ago, naval intelligence traced an al-Qaeda cell operating inside several navy bases in Karachi, the country’s largest city and key port.

“Islamic sentiments are common in the armed forces,” a senior navy official told Asia Times Online on the condition of anonymity as he is not authorized to speak to the media.

“We never felt threatened by that. All armed forces around the world, whether American, British or Indian, take some inspiration from religion to motivate their cadre against the enemy. Pakistan came into existence on the two-nation theory that Hindus and Muslims are two separate nations and therefore no one can separate Islam and Islamic sentiment from the armed forces of Pakistan,” the official said.

“Nonetheless, we observed an uneasy grouping on different naval bases in Karachi. While nobody can obstruct armed forces personnel for rendering religious rituals or studying Islam, the grouping [we observed] was against the discipline of the armed forces. That was the beginning of an intelligence operation in the navy to check for unscrupulous activities.”

The official explained the grouping was against the leadership of the armed forces and opposed to its nexus with the United States against Islamic militancy. When some messages were intercepted hinting at attacks on visiting American officials, intelligence had good reason to take action and after careful evaluation at least 10 people – mostly from the lower cadre – were arrested in a series of operations.

“That was the beginning of huge trouble,” the official said. [Continue reading…]

Pepe Escobar, a fellow correspondent for Asia Times, describes Shahzad as “a brother.”

In the aftermath of 9/11 we worked in tandem; he was in Karachi, I was in Islamabad/Peshawar. After the US ”victory” in Afghanistan I went to visit him at home. He plunged me into Karachi’s wild side – in this and other visits. During a night walk on the beach he confessed his dream; he wanted to be Pakistan bureau chief for Asia Times, which he regarded as the K2 of journalism. He got it.

And then, years before ”AfPak” was invented, he found his perfect beat – the intersection between the ISI, the myriad Taliban factions on both sides of AfPak, and all sorts of jihadi eruptions. That was his sterling beat; and no one could bring more hardcore news from the heart of hardcore than Saleem.

I had met some of his sources in Islamabad and Karachi – but over the years he kept excavating deeper and deeper into the shadows. Sometimes we seriously debated over e-mails – I feared some dodgy/devious ISI strands were playing him while he always vouched for his sources.

Cornered by the law of the jungle, no wonder most of my Pakistani friends, during the 2000s, became exiles in the United States or Canada. Saleem stayed – threats and all, the only concession relocating from Karachi to Islamabad.

Now they finally got him. Not an al-Qaeda or jihadi connection. Not a tribal or Taliban connection, be it Mullah Omar or Tehrik-i-Taliban Pakistan. It had to be the ISI – as he knew, and told us, all along.

Shahzad had just published a book, Inside Al-Qaeda and the Taliban: Beyond Bin Laden and 9/11.

In an interview on the Real News Network recorded a few days before his murder, Shahzad described the transformation of al Qaeda over the last decade and that while the group itself has shrunk, its ideology has spread horizontally by incorporation inside and beyond the new Taliban.

First you have to understand this fact, that there are 17 Arab-Afghan groups which are operating inside Pakistani tribal areas and in Afghanistan, and most of these groups and most of the groups are aligned with al Qaeda but they are not part of al Qaeda — number one. And the strength of those 17 Arab-Afghan groups is over 1,000 approximately.

Second, those who are the members of al Qaeda are hardly 100, not more than 100.

The third thing is — and this is the most important thing — and that is the phenomenon of new Taliban — the new generation of those Afghan fighters, of the Pakistani fighters, or the fighters coming from the Pakistani tribal areas who previously pledged their allegiance to Mullah Omar and the Taliban, but now they — in the last ten years — they completely absorbed al Qaeda’s ideology inside-out, and they are more loyal to al Qaeda than to Mullah Omar or to the al Qaeda leaders, or to their jihadi commanders.

So this is the new group, this is al Qaeda horizontally, not only in Pakistan, Afghanistan, and the tribal areas, but all across the globe, like in Yemen, in Somalia and other parts, even in Europe, even in America. So this is the new generation on which al Qaeda is heavily banking on. And not only those, but it also includes the new converts, white Caucasians which are living in North Waziristan and in South Waziristan. And many of them were sent back to their countries of origin in Europe, Canada and America, and different countries. So, this was a completely new phenomenon. Al Qaeda grew horizontally in different directions.

Watch Shahzad’s last interview (in two parts) with the Real News Network: