President Musharraf’s resignation has serious repercussions for the US-led War on Terror.

Although he had been sidelined by the Pakistani Army for quite some time before his resignation, the President remained actively involved in running the country's counter-terrorism policy with the military and was still a valuable ally for the United States.

A lynchpin of his country's alliance with the West, Mr Musharraf departure has come at a crucial moment in the battle against al-Qaeda and Taleban insurgents in the region. As he announced his resignation, thousands of Pakistani troops were engaged in fighting Islamist militants who now effectively control the country's lawless tribal region and large swath of North West Frontier Province.

It was, therefore, not surprising that news of Mr Musharraf’s resignation was greeted with glee by Islamist militants fighting in the region.

Maulvi Mohammed Omar, a spokesman for the Tehrik-e-Taleban Pakistan, led by Baitullah Mehsud, declared it was day of jubilation for Muslims all over the world. Hundreds of Islamists and former pupils of the radical Red Mosque madrassa, which was raided by the military last year, offered prayers outside parliament following his resignation. Last week, Ayman Al Zawahiri, the second in command of Osama bin Laden, called upon Pakistani to launch a jihad against Mr Musharraf.

The West will hope that the President's resignation does not weaken Pakistan in its battle with worldwide extremists. For almost nine years, the former military commander had provided the divided country with strong - if highly controversial - leadership. After the September 11 attacks, he built a new alliance with the United States, making Pakistan a crucial cog in the so-called War on Terror. Crucially, he abandoned his government’s long standing support for the Taleban government in Afghanistan, which led to its quick fall at the hands of US-led coalition forces.

In the months and years after September 11, Mr Musharraf's government had a crucial role in fighting al-Qaeda. His forces captured more than 600 Islamist activists, including leaders like Khalid Shaikh Mohammed and Ramzi bin al-Shibh, two alleged masterminds of September 11. Mr Musharraf also banned Islamic militant groups which had once been patronised by Pakistani military intelligence.

The arrests and crackdowns on Islamist groups almost cost Mr Musharraf his life. He narrowly escaped two assassination attempts in 2003 involving al-Qaeda backed Islamic militants.

His political exit robs the West of a stalwart ally who echoed its concerns about how Islamic militancy is destabilising Afghanistan and Pakistan, where al-Qaeda and the Taleban have regained strength. It is from the Pakistani tribal areas, the US and Britain say, that Taleban fighters cross into Afghanistan where they present a real danger to Nato forces.

Today's development may result in further fragmentation of power, which had started after February's parliamentary elections. Following those polls, the country is now ruled by coalition government whose future is uncertain and whose ability to combat extremism in the tribal areas is untested. Nobody yet knows who the next president will be. Led by the Pakistan People’s Party, the civilian government has failed to provide any indication of its foreign policy, leaving its final decision to the military. There is no agreement in the ruling alliance on how to counter militancy and extremism.

While the Pakistan People’s Party, which is the senior partner in the four-party coalition, favours continuing Mr Musharraf’s policy of cooperation with the United States, the Pakistan Muslim League (N), led Nawaz Sharif, wants to review this. However, some analysts believe an elected civilian government could, in fact, provide a surer basis for future action than the weakened Mr Musharraf.

A great deal also depends, as always in Pakistan, on the will of the military. The West is believed to be satisfied that the Army chief, General Ashfaq Kayani, is fully committed to following his predecessor’s policy. However, it still faces a huge task in the border regions. The future for Pakistan is, thus, uncertain.

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