In the wake of “11/5,” the attack at Fort Hood, Barack Obama faces a tough choice--like it or not.

The 44th president must choose to confront an unpleasant reality, head on--or else it will run him over. The issue is the threat of terrorist violence, here on the homefront.

Terrorism, and the debate over how to respond to terrorism, was the defining issue of the 43rd presidency. And now it’s apparent that Obama, too, will spend the bulk of his presidency confronting terror, from Afghanistan to new battlezones, such as central Texas.

Obama and fellow Democrats would rather, of course, talk about health care. But over the next few years, the Fort Hood shooting is going to be a bigger story, since it is connected to our relations, good and bad, with the entire Islamic world, including nuclear Pakistan and almost- nuclear Iran.

For his sake, and for ours, Obama needs to understand that sometimes even presidents don’t get to decide the agenda -- the agenda is decided for him. In such a situation, the question is whether or not the president can adapt to the new era and its new challenges.

So this president needs to launch an aggressive investigation, digging into every aspect of Thursday’s shooting rampage that left 13 dead and dozens injured. How did it happen? Who bears responsibility? And, most importantly, what must we change now? Otherwise, if Obama simply talks about health care and “cap-and-trade” and “don’t ask, don’t tell” and all the other staples of his 2008 agenda, he will be left in the dust by the cyclonic events of 2009 and beyond. And in the wake of the 11/5 shootings, his presidency could be blown away by a whirlwind of damaging leaks, embarrasing reports, and well-justified fears.

Obama will always have his base of support, of course, especially in the media. Taking their cues, as ever, from the siren song of secular liberalism, the Mainstream Media would rather talk about health care, with an occasional digression into gay marriage. As documented by the Media Research Center, MSM reporters are mostly loathe to draw anything outher than politically correct conclusions about the religious and ethnic dimensions of the Fort Hood mass murder.

Thus the MSM is likely to be left in the dust by more fearless, more energetic media. Columnists Dick Morris and Eileen McGann were blunt in their e-mail headline: “Ft. Hood Attack Was Terrorism.” And also on Sunday morning, the top dozen headlines at WorldNetDaily, a popular conservative Web site, dealt forcefully with Fort Hood. So while the MSM is bemoaning “stress,” “PTSD,” and “over-extension,” WorldNetDaily is offering an entirely different narrative, featuring headlines such as “Muslims: ‘America’s chickens have come to roost,’ U.S. Islamic street preachers declare Fort Hood victims got just desserts,” and “Shooter advised Obama Transition: Fort Hood triggerman aided team on Homeland Security task force,” and “Military jihadists fill ‘every branch’: Ultimate 5th column penetration, warns best-selling ‘Muslim Mafia’ [author]” One additional piece was penned by Joseph Farah, the Arab-American editor of WND, whose headline blared, “PC sickness killed our soldiers.” How will the commander-in-chief react to that?

Having bungled his first public remarks after the news of the killings at Fort Hood, Obama is already on the defensive. So, most likely, he and his staff will seek to change the subject as quickly as possible.

But if they try doing that, getting back to, say, “the public option,” they will fail. Because the issue isn’t going away. As Georgetown University terrorism expert Bruce Hoffman said over the weekend:

“I’m not saying it’s part of an organized campaign or a systematic strategy, but we're seeing a sea change when we have once a month a plot that is related somehow to Afghanistan, Iraq or what these people see is a war against Islam. It's too easy to dismiss them as unstable individuals when they have expressed strong religious beliefs with politics. That's the essence of the radicalization we're facing.”

In other words, Fort Hood was not a random event; it was part of a pattern.

The irony is that Obama could dominate the counter-terrorism issue, if he wanted to. The president has the governing tools that might really make a difference; he oversees the entire Department of Defense, the Department of Homeland Security, and the Justice Department -- including the FBI. If he uses his vast authority to force a thorough, let-the-chips-fall-where-they-may investigation, demanding full accountability while chasing down every last lead and angle, the American people, most of them, will feel reassured.

But if he allows the bureaucracy to cover its own collective posterior, if he fails to force meaningful reform on the system, if he accepts a “lone gunman” thesis, then America will be convulsed with mistrust, even paranoia. Unfortunately, Obama, whose resume includes no executive experience before becoming president, seems singularly ill-equipped to ride herd over a sprawling bureaucracy.

And if the bureaucrats mislead Obama, and if he passes along their misleading conclusions to the American people -- it will be Obama who gets blamed. The buck stops with him. He won’t be able to hide behind his TelePrompter.

Meanwhile, others, more determined to find answers, and less worried about upsetting the apple cart, will be pressing ahead. One such person who is already leading the charge is Sen. Joe Lieberman, chairman of the Homeland Security Committee. He has already announced that he will be launching his own investigation. Lieberman, a former Democrat and now an independent, endorsed John McCain in the election last year, in large measure because he mistrusted Obama on national security. And for their part, the Obamans probably dislike Lieberman more than any politician this side of Joe Wilson. So expect a rancorous inquiry.

But to the American people, the issue isn’t Lieberman, or any politico. The huge looming issue is security for America. We went through a period similar to this in the 1940s, when Americans started to fear that the establishment, led by a Democratic president, was not being sufficiently vigilant about the threat posed by communism. Those concerns, rational and irrational, soon cost the Democrats the presidency; indeed, they vexed American politics for the next four decades.

Now communism is gone, but Islamic radicalism and jihadism are with us. Obama will have to find an effective way to deal with this new threat or the American people will find someone else who can.

James P. Pinkerton is a Fox News contributor.