As the United States and its Afghan allies wind up their war in Afghanistan, Pakistani President Gen. Pervez Musharraf is just beginning a very different kind of war here in Pakistan.
Starting on Jan. 12, when President Musharraf banned many Islamic militant groups and began the reorganization of his top spy agency, Pakistani radicals, clerics, terrorists, and perhaps even rogue members of Pakistan's own intelligence agencies, have gone underground to regroup. Some observers say that last month's kidnapping of Daniel Pearl, an American reporter for The Wall Street Journal, and this week's foiled rocket attack on US Air Force hangars at Karachi airport, may be the first steps in a long, ugly backlash against Musharraf's crackdown.
But Musharraf's success will largely rest on his ability to maintain loyalty from the powerful Inter-Services Intelligence agency (ISI), the spy wing of Pakistan's three armed services. A quiet and massive overhaul of the ISI has reportedly begun this week.
"The biggest problem we have here are the rogue elements in the intelligence agencies, especially those who at some time became involved with the CIA," says a senior military source who once served in ISI and spoke on condition of anonymity. Even honest ISI agents are used to doing things their way, he says. "In the Soviet war in Afghanistan, the CIA had just preferred taking the backseat and allowing ISI to run the Afghan thing."
For Musharraf, fighting a war on terrorism requires the full cooperation of all law enforcement, military, and intelligence agencies. To consolidate his control and guarantee loyalty, Musharraf is believed to have disbanded ISI units that worked with militant groups and replaced top ISI generals with personal friends. Yet a small group of ISI agents at the ground level may still have the ability either to break the back of Islamic militancy or quietly foster it indefinitely. A few rogue spies may even be helping the very people that have kidnapped Daniel Pearl.
No one knows for sure how how many agents the ISI employs. Its power is not so much seen as felt. Places where foreigners congregate - such as important Pakistani ministries, major hotels, and even taxi stands - generally have ISI agents on staff to monitor activities.
Most ISI agents are soldiers, sailors, or airmen who are temporarily assigned to the ISI for a two-year period, but some have been assigned to a single project for decades, even until retirement.
Among the more dangerous, sources say, are those who acted as Pakistan's official liaison between the Pakistan Army and militant groups, such as the Kashmiri-oriented Harkatul Mujahideen and Lashkar-e-Tayyaba, both of which are on the United States' list of terrorist organizations. The ISI was also a crucial link between Pakistan and the Taliban in Afghanistan.
Getting ISI agents to change direction swiftly would be difficult, the senior military source says, and some may be willfully disobeying orders. Pakistani officials say there is no evidence to suggest that ISI is currently aiding the kidnappers of Mr. Pearl, but there is no question that anyone who investigates the ties between Al Qaeda and Pakistani religious parties and even the ISI is doing so at their own peril.
"Remember, feelings are still so raw, and chasing Al Qaeda is like trailing a wounded tiger," says the senior military source.
Musharraf may be risking the ire of that wounded tiger himself. In the wake of his Jan. 12 speech, cutting all ties to Kashmiri and other militant groups, Musharraf ordered the arrests of dozens of leaders of Pakistan's small but influential religious parties. Most important, he is believed to have began a massive reorganization of the ISI, shutting down the units that coordinated activities in Afghanistan and Indian-controlled Kashmir. The Kashmir unit, in particular, had close ties with radical Islamic groups such as the Harkatul Mujahideen and Jaish-e-Muhammad, both of which trained recruits in Al Qaeda training camps.
The chief suspect in the Pearl kidnapping, Ahmad Omar Saeed Sheikh, is a top leader within Jaish-e-Muhammad.
Yesterday, Fahad Naseem confessed in a Karachi court that he sent e-mails that announced the kidnapping of Pearl. Mr. Naseem told the judge that Mr. Saeed ordered him to send the e-mail and that there were plans to abduct someone who was "anti-Islam, and a Jew."
While some here worry that the Pearl kidnapping is a sign that Musharraf could be losing the support of his own military because of his antiextremist crackdown, others say there are few signs of trouble so far.
"I'm surprised that more hasn't happened actually," says Mushahid Hussein, former information minister under Nawaz Sharif, Pakistan's twice-deposed prime minister. "This guy is reshaping alliances with Afghanistan, restructuring the Pakistani military. There have been U-turns on all of these, but no backlash that you can talk about. The people of Pakistan have a better understanding of why Musharraf has done what he has done."
As for the Pakistani Army, which during the 1980s lowered its educational standards for admission and recruited staunch Muslims, Mr. Hussein says soldiers and officers will remain "strongly disciplined" and loyal to Musharraf, their commander in chief.
Even with this support, the duration of Pearl's disappearance is a thorn in Musharraf's side. Pakistani police admit that they have reached a dead end in their search for Pearl and his captors.
Pakistani officials say that the investigation will continue "with the same intensity and vigor" as before, and that the interrogation of Mr. Sheikh has revealed little. Abir Rashid Khan, spokesman for the Pakistani Interior Ministry says police are operating under the assumption that Pearl is alive. "So far, that is the assumption," he says.
Pearl's disappearance is much different than the hundreds of kidnappings of Pakistani journalists that have occurred in the past 50 years, which used traditional ploys of intimidation, extortion, or ransom notes.
As an investigative reporter delving into the financial ties between Al Qaeda and religious parties here, Pearl may have touched a raw nerve among the people he was investigating. As an American in Pakistan, Pearl may have presented a target of revenge and a chance to embarrass Musharraf in front of his US allies. And at a time when many Pakistani extremist leaders remain behind bars, Pearl may still be a valuable bargaining chip for the people who lured him into captivity a month ago.
"It's a tremendous act of defiance," says Rifaat Hussein, a political scientist at Quaid-I-Azam University in Islamabad. "Despite all the punishment they have gotten and the arrests, [militant groups] still are capable of doing something like this."
"Obviously, there's a much larger chain of people involved in this kidnapping," Dr. Hussein adds. "These are biological self-producing cells."