Using the Cryptographic Sequencer throughout the game, the player can find three hidden radio waves that transmit numbers.
These series of number can be deciphered with different mathematic methods, revealing a series of numbers, which need to be deciphered by correlating the numbers to letters of the alphabet.
Spoiler:These codes read out "I Will Return Batman", "You Will Pay For What You Have Done To Me", and "Fear Will Tear Gotham City To Shreds". The methods used to obtain these results, and their context, suggests that Scarecrow would return, which he would eventually do as the main antagonist of the 2015 game "Batman: Arkham Knight".
Contributed by Funland47