Andrew Buncombe: A big heart, a brave soul and a death that leaves some blood on our hands

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Syed Saleem Shahzad had strong hands.

When he took hold of one of yours and clasped it enthusiastically you wondered what damage might be done. It was just that way three weeks ago in Islamabad, in the aftermath of the US operation to kill Osama bin Laden. There was the broad smile, the laughter, the luxuriant beard and the strong grip. "How have you been?" he said, as we got into his Toyota Corolla.

He'd recommended a newly opened café, but we ended up in Kohsar Market, gathered at a window seat in a coffee shop called Gloria Jean's, overlooking the spot where Salmaan Taseer, the governor of Punjab province, had been gunned down earlier in the year. I had not seen Saleem since he himself had been shot; attacked last summer by a mentally unstable guard outside the UN club. He'd also been badly injured in a car crash a few months ago while returning from a reporting trip in South Waziristan; indeed, the reason he had not travelled to Abbottabad to cover Bin Laden's death, was that the three-hour car journey required to get there would have been too painful.

After he'd pointed out where, on his right side, he'd been shot and where a fragment of the bullet was still lodged and described the ongoing stiffness from the accident, we got on to Bin Laden. Saleem believed the compound in which he was found was a safe house operated by Pakistan's Inter-Services Intelligence (ISI) agency. As we swapped ideas, he also let slip that he'd been called in by the ISI last October when they asked him about his sources for an earlier article. He revealed things had been said to him that could have been taken as a threat.

We now know Saleem took the threat seriously enough to send an email to Ali Dayan Hasan of Human Rights Watch, in which he recounted that one ISI official, Rear Admiral Adnan Nazir, had concluded the October meeting by saying: "We recently arrested a terrorist and recovered a lot of ... material. The terrorist had a hit list with him. If I find your name in the list, I will certainly let you know."

Saleem went missing en route to a television studio to discuss an article he had written for Asia Times Online, in which he highlighted alleged infiltration of the Mehran naval base in Karachi by al-Qa'ida. HRW says it has credible evidence he was picked up by the ISI. Two days later his battered body was discovered in a shallow canal by locals in Mandi Bahauddin, 100 miles south of Islamabad.

Given what transpired, of course, the meeting with the ISI and the message he was given look sinister. But in Gloria Jean's, sipping our coffee, Saleem appeared to make light of it. He was laughing and smiling as always. He had received threats before, but he was not overly troubled. Few can feel that way now. Pakistan had already earned the unwanted distinction of being the most dangerous place for reporters. Eleven media workers were killed there in 2010. For local reporters the situation is particularly perilous, and even working for an international media organisation is no protection against harassment, beatings and murder. The killing of the 40-year-old, who was married with three young children, has delivered the most chilling message. As one Pakistani commentator put it: "The deeper recesses of the security state will yet again be probed more hesitantly."

I'd first met Saleem four years ago. It was my first trip to Pakistan, and we'd arranged to meet in Islamabad's 'Kabul' restaurant. Famed for its kebabs and large Afghani naans, and where meals are completed with cups of green tea, we ordered too much food. During the evening, he recounted his trips to Afghanistan and Pakistan's tribal areas. It was clear he operated in a murky, often Janus-faced environment and had extensive contacts both with the ISI and among militants. He'd interviewed Baitullah Mehsud and Ilyas Kashmiri. A few months later he hosted a lunch at his home in Karachi (where he was based before subsequently moving full-time to Islamabad). It was the weekend after Benazir Bhutto's return to Pakistan (a homecoming that turned into a bloodbath), and on that afternoon in his modest apartment, not far from the ocean at Clifton, he and his friends tucked into mutton biriyani – once again, there was far too much food – and shared their views on who was behind the blast on Bhutto's convoy. It was an insight that this was a country where the most outlandish theory was often the most popular.

Not everyone liked Saleem's reporting. Once I joked I needed a flow chart to follow some of the twists he narrated. But no one could doubt his commitment to covering issues few others did. Many turned to him for insights and he was generous with his time, thoughts and contact numbers. As one of his friends, someone who has known him for 20 years and who this week collected his body from the police station in Mandi Bahauddin, put it: "He never compromised his stories. He always tried to paint a true picture, and this is the punishment for his professionalism, for his truth." Few words have deeper relevance to Pakistan than impunity. In recent days, the country has been beset by outrage. Journalists' groups have flown black flags and demanded an inquiry, to which the government has agreed.

The ISI, in a rare public proclamation, denied it was in any way involved, but the writer Mohammed Hanif put his finger on it when he asked on Twitter: "Any journalist here who doesn't believe that it's our intelligence agencies?" The truth, as Saleem's friends know, is that, whatever outrage they may feel, it's almost certain the perpetrators will never be found. Saleem was the sixth Pakistani journalist to lose his life this year. He is unlikely to be the last.

Does the West have a role in any of this? Of course. The US and Britain have consistently set aside human rights in their dealings with Pakistan. Dictators have been backed in the name of stability, disappearances have been ignored or colluded with as part of the "war on terror", outrages have been overlooked in Balochistan. Wikileaks revealed last year that when the US learnt Pakistani forces were operating death squads against suspected militants in Swat, it took a decision not to speak out publicly. And all the while the billions in military aid keep flowing. It would be refreshing if, just once, a visiting US army chief would raise with his counterpart in Islamabad, not why the Pakistan military was failing to wage war with sufficient vigour against militants, but why it was waging war against its own people.

When news broke that Saleem had gone missing, most assumed he would soon be released. When his Toyota was discovered close to an unidentified body, everyone prayed against the odds for the best. It was not to be. A post-mortem examination has since shown he was tortured to death.

On Tuesday evening, I struggled to sleep, thinking about what he must have endured in those last hours. His sore and still-rehabilitating body bore 15 separate injury marks. His ribs had been broken, his lungs punctured, his liver damaged, his face battered. It was reported there were rope marks on his wrists and ankles, revealing that his hands and feet had most likely been bound. As the blows rained down, he would have been unable to defend himself. Those strong hands would have been of no use.

Andrew Buncombe is The Independent's Asia Correspondent. He was recently awarded the 2011 Amnesty International media prize for reporting.

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