Armored Batsuit
Beat the game once. Can only be used in challenge mode.
Big Head Mode
Take out your cryptographic sequencer and hold [L1] and [R2]. Rotate the right analog clockwise. Do this until Batmans head becomes big. All enemies will have a big head as well.
New Game+
Beat the story mode on Normal or Hard difficulty.
Cryptographic Message
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
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.
Taunt Animation
To make Batman (or any other playable character) execute a taunt like they do in the beginning of a challenge map or round, rotate the right analog stick clockwise two or three times. If you execute a taunt before performing a glide kick, the camera will change into the enemy's perspective during the glide kick action (only works for Batman or Robin).
Easy way to get the Flawless Freeflow Fighter 2.0 Trophy
Go to the Riddlers Challenges and go to Custom Challenge. Select the first map and under modifiers choose Takedown Projectiles. This will make it so that your batarang will knockout enemies in 1 hit. Spam the batarang through all 4 rounds knocking out the enemies without getting hit once and you will get the trophy.
Big Head Mode
Take out the cryptographic sequencer and hold [L1] and [R2]. Rotate the right analog clockwise, do this until Batman's head becomes big - Batman and all enemies will have big heads.
Unlock Additional Game Modes
I Am the Night - Beat New Game Plus.
New Game Plus - Beat the game in Normal Mode or above.
Unlock Skins
1 Million - Link WBID to account.
Blackest Night - Prestiging in Multiplayer.
Dark Knight - Complete All Dark Knight Challenges.
Earth 2 Dark Knight - Connect WBID to Batman Arkham Origins iOS game.
Injustice - Earn all Challenge Mode Medals.
New 52 Graphic - Complete All Most Wanted.
Red Son - Earned by playing iOS game.