The resignation of Pakistan’s president, Pervez Musharraf, raises new concerns about the future course of Pakistan, one of the most important theaters in the war on terror.

Over time, the departure of Musharraf could allow Pakistan’s democracy to deepen, but the near-term outlook is deeply troubling.

With Musharraf gone, the coalition government will be riven by struggles over who will hold the presidency. This comes at a time when the Taliban and al-Qaida are rebuilding and staging increasingly effective attacks in Afghanistan.

After Sept. 11, Musharraf reversed Pakistan’s support of the Taliban and outwardly allied with the United States. He cooperated in the apprehension of Sept. 11 conspirator Khalid Sheikh Mohammed. But his loyalty was always suspect, and the results of his efforts were often marginal.

It was on his watch that the network of A.Q. Khan transmitted nuclear-weapon designs to Libya, North Korea and Iran.

And Pakistan’s Inter-Services Intelligence agency never completely broke relations with Islamic extremists.

Last month, U.S. officials confronted Pakistanis with evidence that the ISI was in on the planning for last month’s terrorist attack on the Indian embassy in Afghanistan.

Musharraf’s undoing was his decision last year to remove Pakistan’s chief justice over the issue of whether Musharraf could legally run for a third term.

Ultimately, Musharraf declared a state of emergency, jailed lawyers and removed several dozen additional judges, but by then he had become marginalized.

For U.S. interests in the region, the immediate outlook is bleak.

Washington should work hard to cultivate allies in the current coalition government, and influence Pakistani policy as best it can.

And Pakistanis should recognize that the future of their own nation depends on their ability to meet the threat posed by Islamic radicals in general, and the Taliban and al-Qaida in particular.