It was a big mess. There'd been warnings for year, but both the Clinton and Bush administrations blew it off.
Under Clinton, there was training where Air Force jets approached civilian planes in a threatening manner. That was a reaction to the threat of civilian planes being hijacked and flown into buildings.
A common thought was that it'd be a "loose nuke" or dirty bomb. They wouldn't even have to clear customs; just set it off in a major harbor or in an aircraft transiting the US from South America to Canada along the Eastern seaboard.
For good measure, the thinking goes, put the nuke in a shipment of drugs. Everyone would be trying to hide it before it even got to port.
I thought that too. As it turns out, a nuke or dirty bomb was difficult for the terrorists to get their hands on.