General Musharraf’s departure from the presidency of Pakistan, which he has held formally or informally since 1999, comes with Pakistan experiencing political instability, terrorist bombings, and separatist campaigns. There is a virtual war over large territories where control has effectively fallen to elements in sympathy with Osama bin Laden. There is a flare up of violence in the part of Hindu India claimed by Muslim Pakistan. Pakistan’s famed and feared Directorate for Inter-Services Intelligence has been accused by the Bush administration of being complicit in the July bombing of the Indian embassy in Kabul.

That’s only part of the problem. The country’s most important foreign relationship beside India, with America, is in tatters. During the more than yearlong crisis that has ended with Mr. Musharraf’s ouster as president, both the State Department and the Pentagon had banked on the general remaining in power. Evidence was leaked indicating that some of the billions of dollars of American aid sent to the Pakistani army for use in attacking the Taliban and Al Qaeda forces hiding in the vast mountainous region between Pakistan and Afghanistan had been diverted.

During a visit to Washington, Prime Minister Gilani offered assurances of continuity in his government’s policies with regard to the Taliban and Al Qaeda forces fighting NATO forces in Afghanistan. But many in the new government in Islamabad do not support the military operations by Pakistani forces in Swat and the Federally Administered Tribal Areas. And there is no gainsaying that Mr. Musharraf was, at least following September 11, 2001, identified closely with a pro-American policy. The relationship is now bound to undergo a change.

A. Q. Khan, the “father of the Islamic bomb,” was released from house arrest although warned not to speak about nuclear proliferation. Apparently the generals feared that Mr. Khan might implicate people still in high office. At least Mr. Khan, if silenced, is alive. A widespread rumor in Pakistan is that Benazir Bhutto was assassinated after telling colleagues that, once elected, she would open the nuclear file. In an interview yesterday in a Singapore newspaper, the Straits Times, India’s national security adviser, M. K. Narayanan, said that many Pakistanis “attribute the killing to ISI.”

Mr. Narayanan said the political instability in Islamabad was of great concern to New Delhi, predicting that Mr. Musharraf’s departure will leave a “big vacuum” that will give freedom to radical extremist elements to do “what they like.” ISI has been involved in the past with Muslim terrorists operating in both Kashmir and in Afghanistan. ISI helped launch the Taliban and supported and protected groups operating in Kashmir.

Jammu and Kashmir remain the focus of Pakistan-India tensions. The territories are heavily populated by Muslims but remained on the Indian side of the border when the subcontinent was partitioned in 1948. Many leading Pakistani Muslims never reconciled themselves to losing Kashmir.

This week, violence flared in the disputed areas and, in an unsuccessful attempt to rally support to his side, Mr. Musharraf used Pakistan’s Independence Day celebration to appeal to the widespread and powerful sentiment about what Pakistanis see as the two Indian-occupied territories. “Every Pakistani is with our brothers and sisters in Srinagar,” Mr. Musharraf said, referring to Jammu-Kashmir’s summer capital. “Kashmir beats in the heart of every Pakistani.”

Mr. Musharraf angered the Indians by condemning the recent violence as “human rights violations” while describing the 21 people killed as a result of the new violence in the Kashmir valley as “martyrs.” To make matters worse, Mr. Musharraf’s remarks on the unrest in Kashmir valley came soon after India repudiated Pakistan’s attempt to internationalize the problem by referring it to the United Nations. India’s government quickly replied that the call for international involvement was “gratuitous” and “illegal.”

As chief of the general staff of the army, Mr. Musharraf came to power almost a decade ago after he nearly triggered a war with India by infiltrating Pakistani troops into the mountains overlooking the Kashmir valley — on the Indian side of the border. He did this without any consultation with the elected prime minister, Mr. Shareef, who is himself no slouch when it comes Muslim solidarity and the Kashmir issue.

It’s hard to predict which way Pakistan will turn. All of the forces unleashed by the upheaval within the Muslim world appear in their most concentrated form in Pakistan: A weak state, nationalism eclipsed by religious and tribal loyalties, an inability to impose the rule of the central government in large areas, and a political class that routinely is unable to address the nation’s problems. That’s why the political history of Pakistan is of a pendulum swinging back and forth between military and civilian rule. Undoubtedly, we have not seen the last of the generals. And undoubtedly, too, one of the issues our next president will want to tackle, along with Iran and Russia and North Korea and China and Europe, will be how to gain Pakistan’s full cooperation against Al Qaeda and prevent its nuclear arsenal from slipping into the wrong hands.