I found this on Cruise Critic - Apparently the Magic was due to head back the next day anyway.
I took my very first cruise on the Disney Magic during 9/11. The Magic was doing a special run that week in which we did a 4 day cruise (Nassau, Freeport, Castaway Cay). We were having a beautiful, restful cruise until the tragedy occurred. The morning of 9/11 we had docked at Castaway Cay. The weather was somewhat dismal in my opinion. It was raining and overcast. I decided to sleep in a bit to wait for the weather to clear. Most cruisers were already at the beach. I was sleeping soundly when my mother woke me telling me a plane had crashed into the World Trade Center. I sat there dazed watching the news when the second plane crashed into the second tower. Then of course the tragedy at the Pentagon and the Pennsylvania crash occurred.
At that time no annoucements were made. We decided to go ahead and get off the ship and go to the beach. Although I was upset we still made the best of it. Most people did not know about the events until they returned that afternoon. Many people were crying watching the news in the lounge. The evening show did go on, but it was a real quiet on board that evening.
Disney did a great job handling everything. As the airports were closed, Disney quickly made arrangements that evening for transportation, lodging and food at the resorts.
Upon returning, all I can recall is that we traveled as quickly as possible back to the port. We had a storm that evening and we rocked and rolled all the way back at top speed. I literally rolled out of the bed. I recall seeing helicopters and lights a we got close to the port. Upon departing the ship, there so many police, military personnel, and dogs on site