But as CBS News Correspondent Lee Cowan reports, a decade later as an advisor to the Department of Homeland Security, Pepe's biggest worry is the cost of terrorism.
Asked how prepared we are, on a scale of one to ten, Pepe says, "If we were at a three or four a couple of years ago, it may be more like a five or six."
Even that's optimistic by some standards. A recent government investigation found that two years after Sept. 11, most urban hospitals "still lack equipment, medical stockpiles and quarantine facilities" to cope with even a small scale biological or chemical attack.
The Council on Foreign Relations put it more bluntly.
"We are not ready for another attack," says Jamie Metzl, the report's author. "We've made important progress since Sept. 11, but there's a big gap between where we are and where we need to be."
The gap will likely only grow wider as hospitals all across the country struggle just to provide daily care.
"You know hospitals and doctors and nurses are not in the business to avoid taking care of people," says Pepe. "We all want to do that, the question is where do we get the funding to do this."
And if major cities are short on funding, rural communities are either farther behind.
Take Glen Rose, Texas, a town of barely 3,000 people.
It's the kind of community that is so small, no one would ever think to put it on a terrorist's hit list, were it not for its two rather conspicuous neighbors: the twin reactors of its nuclear power plant just five miles away.
Despite the potential threat, its small 14-bed hospital received no additional funding until just two weeks ago.
It received $11,000.
"This is basically what we were able to acquire," says Dr. Gary Marks, CEO of Glen Rose Medical Center.
It bought just six chemical suits, boots and gloves and a bio-terrorism poster.
"We don't anticipate any additional funding coming down," says Marks.
Marks says the problem isn't only a lack of funding, but a lack of federal standards on just what being "prepared" means.
"We need the experts to come out here and spend some time with us, to reassure us that what we're doing is correct," he says.
For two years, hospitals have been struggling to prepare for the unthinkable. But short of a massive re-direction of federal funds, thinking about preparedness is all most may be able to do.