This was the last tweet of Syed Saleem Shahzad:

Syed Saleem Shahzad, 40, worked for an Italian news agency and an online news site registered in Hong Kong. He went missing on Sunday after he left his home in the capital to take part in a television talk show, but never arrived.
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He disappeared two days after writing an investigative report in Asia Times Online that al Qaeda carried out last week’s attack on a naval air base to avenge the arrest of naval officials arrested on suspicion of al Qaeda links.Ali Dayan Hasan, senior South Asia researcher at Human Rights Watch, said Shahzad had complained about being threatened by Pakistan’s Inter-Services Intelligence (ISI) agency.
The story about the 'Al-Qaeda' vs. Pakistani Navy he linked in his last tweet is here.
As he tells it, the Pakistani navy found 'Al-Qaeda' friendlies in its ranks and arrested them. The people responsible for the arrests were then threatened and it became clear that more people with inside navy knowledge about the arrests were informing 'Al-Qaeda' about the who, where and what. Naval intelligence then tried to negotiate with 'Al-Qaeda' which demanded the immediate release of the prisoners. On April 22 two navy buses in Karachi were bombed with two dead and some 50 injured. More moles where captured but the threats only increased. Then followed the big attack on the naval base in Karachi on May 22.
Syed Saleem Shahzad report is so far unconfirmed but certainly has some truth in it. That it is the reason why he was tortured and killed is plausible. But who or what part of the Pakistani military or of 'Al-Qaeda' killed him will likely never be known.
In the past I have used many of his stories in my writing here and even while he sometimes tended to dramatize, his sources on all sides of the conflict were excellent and his sometimes seemingly wild stories were often confirmed by other reporting later on.
I'll miss him and the very useful information from the ground of the conflicts in Pakistan he provided. Syed Saleem Shahzad leaves a wife and three children. Buying his just published book Inside Al-Qaeda and the Taliban: Beyond Bin Laden and 9/11 may help them to get through the financial trouble of this loss.