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Cryptographic Message *SPOILERS*
Using the cryptographic Sequencer, set the coordinates to 200, 500. A voice will speak the following numbers: 3-20-26-18-26-16-24-1-11-4-24-9-3-8-5-2-12-18-6-16-7-11-3-10-17-5-13-4-21-8. To decode requires a bit of work. First set each number to a letter in the alphabet but in reverse so that Z=1, Y=2, X=3 and so on. From there you use a special cipher known as a Vigenere Cipher that requires a keyword to translate. By using the keyword "scarecrow", the message is translated to "FEAR WILL TEAR GOTHAM CITY TO SHREDS". Due to the keyword being scarecrow, it could be implied that Scarecrow is behind at least this message and possibly more.
Hidden Message
Use Batman's Cryptographic Sequencer and track down the XY coordinates 700, 490. You'll intercept a radio frequency that reads the following numbers: 9-23-9-12-12-18-5-20-21-18-14-2-1-20-13-1-14 (it will then make a buzz sound and repeat these numbers) When matched to the corresponding letters of the alphabet they spell out I WILL RETURN BATMAN.
Hidden Message *Spoiler*
Using the Cryptographic Sequencer, locate coordinates 500,900. You will intercept a frequency repeating the number sequence "5-15-9-7-21-18-18-14-3-5-24-15-12-7-22-3-10-5-15-9-22-3-8-25-26-15-16-25-10-15-17-25". To decode, 1 = C, 2 = B, 3 = A, 4 = Z, and so on. Decoded, the message reads "YOU WILL PAY FOR WHAT YOU HAVE DONE TO ME".
Scarecrow Hideout
Go on top of a boat near the industrial district (the boat should be near two cranes). While on the boat, take out the cryptographic sequencer and use it. Letters will appear instead of the radio stations. Turn the letters until it reads "City Of Terror." A secret passage on the boat will open. Go down into the boat to find hundreds of roaches, a medical order form addressed to Jonathan Crane, and a Scarecrow victim who will squirm if you zoom in on him.