“The moment I heard the first news about the airline plot, I knew it was just a matter of time until we heard the word Pakistan,” said a US intelligence agent. “Whether it’s 9/11, the Bali bombs, 7/7 and now this, Pakistan is always the connection. That’s gotta raise some questions." The roots of Pakistan’s reputation as a haven for jihadists run deep. It was, after all, in the city of Peshawar that Al-Qaeda was born after ISI, Pakistan’s military intelligence, started to recruit Arabs to fight in the Afghan jihad.

It was ISI that turned the Taliban from a bunch of religious students into a movement that took over Afghanistan. According to Hamid Karzai, president of Afghanistan, ISI continues to provide a safe haven, training them to fight British soldiers in Helmand.

Whose side is Pakistan on? After September 11, when Pakistan’s leadership was given the blunt choice by President Bush — “you’re either with us or against us” — it had little option. The decision to support Bush’s war on terror turned President Pervez Musharraf from a pariah dictator to a feted world leader.

It was a lucrative move. Pakistan has again become one of the biggest recipients of US aid — just as it was during the Afghan war against Soviet occupiers when ISI was the main conduit for arms and funds. Since September 11, America has dismissed $1.5 billion in debt and provided Pakistan with more than $3 billion in military assistance.

Last year Pakistan was one of the world’s fastest-growing economies. It recently placed a $2.5 billion order for American F-16 jet fighters — as much as Afghanistan’s entire annual foreign aid.

However, Musharraf has been walking a tightrope. At home he has been the target of three assassination attempts and much criticism, while abroad his commitment is under increasing question.

Critics point out that the six top Al-Qaeda officials so far captured, including Khalid Shaikh Mohammad (KSM), the mastermind of 9/11, were all arrested in Pakistan. They were not hiding in caves but living in cities like Karachi and Faisalabad. KSM was picked up in the military cantonment of Rawalpindi.

It was in Pakistan where Daniel Pearl, the Wall Street Journal reporter, was murdered in 2002. Pakistan has refused to extradite Omar Saeed Sheikh, the British-born Muslim convicted of the killing, prompting speculation that it fears what he might say.

Sheikh was in ISI custody for a week before the FBI was informed and is reported to have given himself up to his former ISI handler. We also know from official reports that two of the July 7 bombers, Shehzad Tanweer and Mohammad Sidique Khan, travelled to Pakistan.

It was Khan’s second trip. It is still unclear what they did there, but British intelligence believes they underwent training and made martyrdom tapes. What is certain is that on their return the pair rented a place to build bombs.

Pakistan’s problem is that extremist organisations and training camps, such as those linked to the London bombers, were either created by, or supported and used by, ISI.

The camps were set up in the late 1980s with US backing to train fighters for jihad in Afghanistan. Their mission was expanded in the 1990s to send jihadis to the contested province of Kashmir to fight a proxy war with India.

Explore UK News

• Crime News

• Education News

• Health News

• Science News

• Scotland News

Times Recommends

• Brown gambles it all on rescue plan
• Motherhood boosts female brain power
• That's no old FT, that's my naked wife