The Pakistanis could call out the entire army, and go to war with the Pushtun tribes. This, however, would be enormously expensive politically, and in terms of soldiers and civilians killed. As it is, the Pakistanis are exercising more presence in the tribal areas, and more pressure on the tribes, than at any time in history. The Pushtuns have been resisting foreign (non-Pushtun) influence and control for centuries. Before Pakistan was created in 1947, the British had made deals with the Pushtun tribes, to try and reduce the raids into non-tribal areas. Pakistan continued those deals, while slowly moving government control into urban areas within the tribal territories. But, by law and ancient custom, the tribes were still very autonomous. Under pressure from the United States, that has changed.
Al Qaeda declared war on the government of Pakistan three years ago, and that was used as an excuse to come into the tribal territories looking for the terrorists. But al Qaeda are also considered "holy warriors" by the religiously conservative Pushtuns. Thus, many of the tribesmen feel honor bound to defend their al Qaeda guests. So, at the moment, the Pakistanis are caught between the need to keep al Qaeda under control in Pakistan, and avoiding a civil war with the Pushtun tribes.
Meanwhile, more Islamic terror groups, or factions of them, are openly joining forces with al Qaeda. This includes Egyptians and Palestinians. There are also signs that al Qaeda is trying to raise local support in various parts of Africa (Sudan, Nigeria, Somalia, Southeast Asia and Morocco). These "affiliates" are in it for the publicity, and any practical help they can get in carrying out local acts of terrorism. Al Qaeda has positioned itself as the extremists extremist. While officially backing away from attacks that put Moslem women and children at risk, al Qaeda does not explicitly forbid such things. Al Qaeda likes to point out that such attacks are counterproductive, but does not condemn any al Qaeda affiliate that becomes that violent. Al Qaeda police appears to be that the locals will learn, from local backlash, the errors of their ways.
Al Qaeda is desperate to get established in some places where training and planning can safely take place. Some of this work has been possible in the Pakistani tribal areas, but the Pakistani army and security services make it very dangerous to move in and out of that sanctuary. Somalia is turning into another sanctuary, but one that is full of people you can't trust, and can be depended on to give you up if the Americans put the heat on. Same situation in Sudan, Nigeria and Southeast Asia (Philippines, Indonesia, Malaysia, southern Thailand). Morocco also has a dangerous, for terrorists, security service.
For the moment, al Qaeda seems to be spreading cash, and encouragement, in many places, but putting most of its resources into the Pushtun areas (both in Afghanistan and Pakistan.) The growth of the heroin production and smuggling business in Afghanistan has a good chance of turning much of the country into fiefdoms controlled by drug rich warlords. These guys were willing to provide support for al Qaeda in the 1990s, and seem ready to deal again. This explains why the Taliban have some much more guns, money and motivation this year.
Iraq turned out to be a disaster for al Qaeda. The local, largely self-appointed al Qaeda leader. Abu Musab al Zarqawi, was mainly into killing lots of Shia civilians, in an attempt to goad the Shia into a civil war with the Sunni Arabs. While the Sunni Arabs are a majority (90 percent) of all Moslems worldwide, in Iraq, the Shia outnumber the Sunni Arabs by three to one. Moreover, the Shia have more guns, control the government, and have the Americans to back them up. All Zarqawi was able to do was make al Qaeda the most hated organization in Iraq. Eventually, this distaste for Zarqawi's methods translated into much lower popularity ratings for al Qaeda throughout the Arab world. So Iraq is not a likely sanctuary for al Qaeda.
Neither is Saudi Arabia. Al Qaeda fans in Saudi Arabia, enraged at the American invasion of Iraq, began a bombing campaign in Saudi Arabia. While Saudi Arabia had long been a prime source of recruits and money, that stopped real quick as most Saudis turned on the terrorists. It was one thing to cheer on al Qaeda as they killed infidels overseas, but killing Moslems within Saudi Arabia was another matter.
There are thousands of Moslems out there who believe they are part of al Qaeda, and many of them, to one degree or another, actually are. But there are few places where al Qaeda can safely meet, and no place where they can openly congregate. Even in the Pushtun tribal areas, discretion is necessary. As long as American or Pakistani commandos are in the region, al Qaeda cannot rest, only pause and catch their breath.
Where is al Qaeda? A growing body of evidence, and captured members and documents, points to the Pushtun tribal areas of northwest Pakistan. Just across the border from where al Qaeda was based before 2002. Al Qaeda attempts to find refuge in other parts of the world have largely failed. While al Qaeda has appointed many local Islamic terrorist organizations as "part of al Qaeda," the core leaders and staff who fled Afghanistan in late 2001, are still hiding out in the hills along the Afghan border. Despite efforts by the Pakistani army and paramilitary forces, there are still many areas of the northwest where you can hide Islamic extremists. The army has caught several hundred al Qaeda members moving in and out of the area. But for those that stay within the Pushtun tribal areas of Pakistan, there's no easy way to find them, or arrest them.