#1. Intellegence. Lots of it. Bug the homes of any and all suspected terrorists anywhere in the world, including the USA.
#2. Profile those would be terrorists and create a large database and track all their movements, conversations, connections, etc. Of course we would have their houses bugged and have people working inside of their communities. It would be extensive intelligence.
#3. If a terrorist plot is uncovered, make that gentleman disappear.
Have a nice stately 50 year old gentleman go to the front door at 3a.m. and pump him full of bullets. Of course we could come up with many creative ways to eliminate those who make threats. Just making a terrorist threat would be reason enough for deadly force. Those terrorist organizations, all of them, would be targets. Participation in WTC would not be a requirement.
Take the body and wrap it up in chains and dump it 5 miles off shore.
If anyone asks, deny everything.
Of course there should also be increased airport security, etc etc.
Isn't Sean Connery more like 60 years old? :-)