When Secretary of State Hillary Clinton raised the possibility in April of Islamist militants taking over Pakistan and its nuclear weapons, her words were dismissed as alarmist - and perhaps deliberately so as a way of putting pressure on Islamabad to act.

The problem with Pakistan is that it is almost impossible to come up with a view that is not either alarmist or complacent. It is such a complex country that nobody can agree a frame of reference for assessing the risk. It is the base for a bewildering array of militants including Afghan and Pakistani Taliban, al Qaeda and anti-India groups, yet also has a powerful and professional army which would be expected to defend to the last its Punjab heartland and nuclear weapons against a jihadi takeover.  Its potent mix of poverty and Islamist sympathies among a significant section of the population make it ripe for revolution, yet it also has a strong and secular-minded civil society which was willing to go out into the streets earlier this year to demand an independent judiciary.

You can assess the risk in Pakistan by looking at the rate of decline in stability there, and that was faster than anyone expected over the past year or so until a military offensive against the Taliban in Swat  which began in April halted the slide.

Or you can look at the worst case scenario, of Islamist militants taking over a nuclear-armed Pakistan, and decide that even if that outcome is unlikely, the potential dangers arising from it are so great as to put Pakistani stability at the top of global risks.

In an essay in the National Interest, Bruce Riedel, the former CIA officer who led a review of strategy in Afghanistan and Pakistan for President Barack Obama, lays out the implications of that worst case scenario.

“A jihadist Pakistan would be the most serious threat to the United States since the end of the Cold War.  Aligned with al-Qaeda and armed with nuclear weapons, the Islamic Emirate of Pakistan would be a nightmare. U.S. options for dealing with it would all be bad,” he writes.

And if the United States were to try to invade “the Pakistanis would, of course, use their nuclear weapons to defend themselves. While they do not have delivery systems capable of reaching America, they could certainly destroy cities and bases in Afghanistan, India, the Gulf states and, if smuggled out ahead of time by terrorists, perhaps the United States. A victory in such a conflict would be Pyrrhic indeed.

“Of course, the hardest problem would be the day after. What would we do with a country twice the size of California with enormous poverty, almost 50 percent illiteracy and intense popular hatred for all that we stand for after we have fought a nuclear war to occupy it?”

Riedel’s essay, titled “Armageddon in Islamabad” goes some way to answering the oft-asked question of why western troops are fighting in Afghanistan when al Qaeda and its allies are believed to be based in Pakistan. It also helps explain why the United States is so keen to see a peace deal with India that might help stabilise the country.

“A jihadist, nuclear-armed Pakistan is a scenario we need to avoid at all costs,” he says. That means working with the Pakistan we have today to try to improve its spotty record on terrorism and proliferation. There is good reason for pessimism. Working with the existing order in Pakistan may not succeed. But there is every reason to try, given the horrors of the alternative.”

Do read it in conjunction with this article in the CTC Sentinel (pdf), in which Shaun Gregory, a professor at Britain’s Bradford University, assesses the risk of Pakistan’s nuclear weapons falling into the hands of Islamist militants. The nuclear weapons, he argues, are well guarded by the Pakistan Army against the internal threat of a seizure by Islamist militants. But this also means that they could not be spirited out of the country by a third party, or destroyed, in the event of a state collapse.