http://en.wikipedia.org/wiki/Digital_Fortress# Code_solution
The code that appears in the end of the book
128-10-93-85-10-128-98-112-6-6-25-126-39-1-68-78
is decrypted by looking at the first letter of the chapter for each number. For example, chapter 128 starts 'When Susan awoke'. The resulting text is:
WECGEWHYAAIORTNU
Decryption is performed using a columnar transposition cipher, termed a "Caesar Square" cipher in the book (this is unrelated to the Caesar cipher). The letters are arranged into a square:
W E C G
E W H Y
A A I O
R T N U
and read from the top down.
WEAREWATCHINGYOU
Add spaces and you get the plaintext,
"We are watching you"
a reference to the NSA's monitoring systems.