I am writing this column en route to Afghanistan and Pakistan.

Of all the pressing foreign-policy items on President Obama’s plate, bar none, AfPak is the most troubling.

The nightmare scenario used by the Bush administration to justify the Iraq war – the possibility that terrorists might obtain nukes – was applied to the wrong country. Iraq had no nukes and no al-Qaida before we invaded, but Pakistan has both.

In Pakistan, there are dozens of nuclear weapons, along with militant Islamists who want to topple the Pakistani and Afghan governments. The Pakistani government has extensive controls in place for its weapons, and U.S. officials think these controls are still solid.

However, Pakistan’s civilian government is weak and its army trained for fighting India, not domestic insurgents.

“The real battleground is not the FATA (the tribal border area) but Pakistan as a whole,” says Shuja Nawaz, an expert on Pakistani security issues at the Atlantic Council. The militants aim “at nothing less than toppling the Pakistani government,” said Ahmed Rashid,

an expert on militancy in the

region.

Moreover, the militants are extending their operations to areas beyond Pakistan’s border lands, where there are no nuclear facilities, toward Pakistan’s heartland in the Punjab, where such facilities are located.

“I’m made nervous by the increasing ability of militants to operate throughout the country,” said Harvard’s Matthew Bunn, one of the top experts on the proliferation of nuclear weapons. What worries him most is that the militants are now “able to coordinate fairly sophisticated strikes in Punjab.”

Under such conditions, one has to ask whether Pakistan’s extensive nuclear controls might possibly be breached.

This confluence of ideological militants plus nukes is the reason Obama has focused so intently on the AfPak border. Some of my readers complained when I called this Obama’s War, noting correctly that he inherited this mess from a Bush administration that failed to stabilize Afghanistan after we ousted the Taliban following 9/11. Instead, the Bush team transferred critical resources to Iraq, where it got bogged down, and left the Taliban and al-Qaida to regroup on the AfPak border.

The mistakes of the last eight years leave Obama no choice but to focus on this very real threat, which will become the military conflict that defines his first term. Thus his effort to clean up the mess he inherited will indubitably become known as Obama’s War.

Already, he is being attacked from the right for planning to do too little, or too much (I get critical e-mails from conservative readers taking both positions), and from the left for getting bogged down in the Afghan “graveyard of empires.” But there are two important questions posed by thoughtful readers that deserve answers:

First, if Pakistan is the problem, why are we sending 21,000 more troops to Afghanistan? And second, in a country that repelled the British and the Soviets, can those troops really help bring stability, or will they create more support for the Taliban?

The answer to the first question is very complex but boils down to this: Pakistan is a sovereign country and we can’t control its direction. We can’t afford to ignore Afghanistan while we try to convince Pakistan that its existential threat lies within, not in New Delhi. If we wait, the Taliban will take control of more and more Afghan territory, and this, in turn, will further destabilize Pakistan.

As to the second question, the key lies with poll numbers that show the vast majority of Afghans reject the harsh tactics and tenets of the Taliban. Obama’s strategy aims to protect villages from the Taliban until U.S. and NATO trainers can build up a larger Afghan army to do the job. It also aims to find ways for Afghan officials and international donors to deliver economic aid more effectively to the grass roots.

Easier said than done, of course. In Iraq, training a new Iraqi army proved far more slow and difficult than we foresaw. In the end, the violence was stemmed (not stopped) largely by local tribal and neighborhood militias. In Afghanistan, the tribal – and governmental – structure has been broken down by decades of war, and deliberate Taliban assassinations.

Whether these structures can be rebuilt, or Afghan governance can be improved, are open questions. How many insurgents are “reconcilable” – in it for money or revenge, not ideology – and can be peeled off from “irreconcilables” is also uncertain. One thing is clear, however: None of the bigger Taliban groupings will sue for peace so long as they think that they are gaining ground, and the other side is faltering.

That’s why I think Obama must try to stabilize Afghanistan, which requires troops, aid, and regional diplomacy. But I won’t pretend that I know the full answers to the questions posed by my readers. That’s why I’m going out there to look for myself, and to report what I find out.

Trudy Rubin is a columnist and editorial board member for The Philadelphia Inquirer. Her e-mail address is: trubin@phillynews.com.