Have al-Qaida and other militant groups wormed into Pakistan's military?
It's an explosive question, considering that Pakistan's armed forces are vital U.S. allies and also guardians of a stockpile of nuclear weapons. And that was the question a Pakistani journalist addressed in an article written shortly before he was murdered last week.
Saleem Shahzad reported on last month's militant attack on a Pakistani naval base in Karachi. He quoted anonymous sources who linked that attack to the discovery of suspected al-Qaida operatives inside the navy itself.
If his story was true, it illustrated a disturbing infiltration of Pakistan's navy. Security officials have affirmed to NPR that a central allegation of the story was true: Pakistan's armed forces have found evidence of al-Qaida figures in their ranks, and a number of men were detained for questioning even before the naval base attack.
The tale of the reporter's death is a major news story in Pakistan. Shahzad disappeared on May 29, and was later found dead in a waterway, disfigured by apparent signs of torture. Suspicion fell on Pakistan's powerful Inter-Services Intelligence agency, or ISI, which had complained to Shahzad about his past reporting. The uproar against the ISI was so widespread that the agency, which almost never makes a public statement, publicly denied a role in the abduction.
We don't know if someone wanted to silence Shahzad (both militants and the authorities have been known to respond brutally to media coverage they didn't like). But his final story, for the website Asia Times, examined an issue that deeply concerns Pakistan's military establishment.
When militants struck the naval base in May, they made it past base security and destroyed two precious electronic surveillance planes. Many news accounts suggested the attackers had inside information about the base, and investigators eventually detained a former Pakistani commando for questioning.
Shahzad's Asia Times report went further, laying out a disturbing backstory that suggested a wider penetration of the military. Well before the naval base attack, Shahzad contended, the navy had detained at least 10 men currently serving in the navy's own ranks and suspected of links to al-Qaida. According to the report, al-Qaida threatened reprisals if the prisoners were not released. The navy was reportedly so concerned that it actually opened talks with al-Qaida. But the navy didn't release the men, and the naval base assault followed.
NPR was unable to verify all the details of Shahzad's final report, but Pakistani security officials did affirm this much: Before the naval base raid, a number of navy personnel were detained on suspicion of links to al-Qaida. These detentions are the latest sign of extremism within the ranks of the military, Pakistan's most powerful institution.
The foundations of this infiltration were laid many years ago.
Retired army Lt. Gen. Javed Ashraf Qazi, a former head of the ISI and now in charge of the defense committee in Pakistan's Senate, said in an interview that the armed forces are still affected by their experience in the 1980s. That's when the Islamist military ruler Zia-ul-Haq was in charge, and the U.S. was sponsoring a "holy war" against Soviet troops occupying nearby Afghanistan.
"Religion was given too much prominence," Qazi said. "And in fact Zia would reward people who showed themselves to be more Islamist, and therefore a lot of people converted toward this thinking, out of conviction or out of necessity."
Some of those same Islamists, or younger people influenced by them, still "may be existing today in the army or other services," Qazi said.
For years, extremists operated with the knowledge and consent of the military leadership. Pakistan sponsored Islamist militants in Afghanistan, as well as in a long fight with India over the disputed state of Kashmir. The government now insists it has ended such policies.
But after their government service, former soldiers and spymasters soon turned to new targets. For example, Ilyas Kashmiri, an ex-commando, went into business for himself, leading his own terrorist organization until his reported death in a drone strike last week.
"You have highly trained people who eventually retire and go back on civilian streets, and they're free to do whatever they like," says Jehangir Karamat, a retired four-star general who once held the highest rank in Pakistan's army, chief of staff. Some are recruited to use their skills.
In recent years, evidence has periodically appeared of Islamists still serving within the armed forces who are acting against their own institution. In 2009, for example, men in military uniforms blasted their way into GHQ, the heavily guarded headquarters of Pakistan's army.
And now comes the detention of men inside the navy. Current and former military officers have said in recent days that the attack on the naval base is even more disturbing to them than the recent failure to find the hiding place of al-Qaida leader Osama bin Laden.
How serious is the infiltration? Lt. Gen. Asif Yasin Malik, who commands troops fighting militants in the far northwest, expresses full confidence in the army's discipline, as well as the military's internal security apparatus; there may be a few problems in an army of half a million men, he says, but not many.
Qazi, the retired general and current senator, says some extremist infiltration is almost inevitable, given that Pakistan's large military draws its troops from many parts of the nation. "All sorts of people make a society," he says.
Pakistan's military is vulnerable to internal enemies precisely because it represents the society it serves — and right now, that society is at war with itself.