Scarecrow may not have featured as a villain in Batman: Arkham City, but the sequel still included secret details and Easter eggs that foreshadowed his return in Batman: Arkham Knight. Some of the references to Scarecrow were easy to find, but others were very well hidden or required some additional work to figure out. All of the Easter eggs indicated the villain was still alive, and they created anticipation and excitement for Scarecrow's return as a key villain in Batman: Arkham Knight.
In Batman: Arkham Asylum, Scarecrow was one of the inmates released by the Joker to distract Batman as he carried out his Titan scheme. After failing to keep Batman in a state of fear, Scarecrow attempts to dump a large bag of fear toxins into the water running beneath the asylum. When Batman arrives to stop him, Killer Croc jumps out of the water and grabs Scarecrow. Batman triggers Killer Croc's shock collar, but he manages to hang on to the Master of Fear and dives into the water with him. After being taken, it seems as if Scarecrow is dead, but Arkham City proves he's still alive and plotting his revenge - a fate that was foreshadowed in one of Batman: Arkham Asylum's three post-credits teases.
The references and clues confirm Scarecrow is still alive, but they also foreshadow the events that take place during Batman: Arkham Knight's main story. Scarecrow even communicates with Batman through a series of radio broadcasts with different ciphers. Although some of the secrets in Batman: Arkham City are very well hidden or challenging to solve, they do a perfect job of setting up the sequel in a subtle but frightening way.
Arkham City - Scarecrow Goons May Be Present During Protocol 10
There are various henchmen that can be found lying on the ground after the start of Protocol 10, but one group in particular bears a weird similarity to Scarecrow. While some speculate that the dead henchmen are a glitch, there are some strong similarities between their clothing and Scarecrow's look. Additionally, they wear masks that are textured like burlap sacks, which is what Scarecrow modifies to complete his haunting appearance. Even if the dead henchmen are glitches and not Scarecrow goons, the fact that they can be found during Protocol 10 as players complete Batman: Arkham City's story has a few implications.
Since Arkham City is meant to contain every criminal in Gotham, regardless of the severity of their crime, it's likely that a few of Scarecrow's followers ended up as prisoners there. They may have been recruiting others or gathering intel on Batman and other supervillains for Scarecrow. When Protocol 10 was initiated, it's possible some Scarecrow henchmen panicked and revealed themselves in an attempt to escape the explosions. Since Scarecrow leaves a few other clues for Batman to find, it's possible he allowed his thugs to still wear clothing similar to his to create some fear and maintain his status amongst Gotham's villains in Batman: Arkham City.
Scarecrow's Old Mask Can Be Found In Batman: Arkham City
There's a riddle in Batman: Arkham City that's centered around Scarecrow and finding his mask. On top of the bridge in Amusement Mile, there are several piles of straw and Scarecrow's old mask in the middle. If Scarecrow's henchmen were in Arkham City, they may have planted it there for Batman to find as a hint or a threat of what was coming. The mask was the easiest Scarecrow-related item to find, but it also gave the least amount of information. Since Scarecrow's mask was probably found before the other references, it was effective in creating just enough intrigue to look for other clues about his return.
Scanning the mask solved the riddle, "If you're afraid, don't be scared to crow about it." This may indicate that other villains, like the Riddler in Batman: Arkham City, knew that Scarecrow was still alive. However, it's also possible that Riddler obtained Scarecrow's old mask by other means and planted it simply to add to the challenges he gave Batman. Regardless of how it got on top of the bridge, the inclusion of Scarecrow's mask was the first indication that he would make another appearance in the series.
Batman: Arkham City Has A Creepy Hidden Scarecrow Easter Egg
Unlike the possibly unintentional henchmen found after Protocol 10, the other secrets hidden around Arkham City confirm that Scarecrow is planning something big. There's a barge in front of the neon North Gotham Dock sign that Batman can enter using the cryptographic sequencer. The password has the highest possible difficulty rating, so there are various combinations of words to try. However, to add to the ominous foreshadowing of Scarecrow's return, "City of Terror" is the password that opens up the hatch on the boat for this subtle Batman: Arkham Easter egg.
Going inside the barge forces a first-person perspective that aids in creating an unsettling atmosphere. There are wooden boxes, crates full of cockroaches, and a man slumped over in a chair. Approaching the man and zooming in triggers a jump scare where he twitches and screams before dying. The invoice to the right of the man indicates that Scarecrow was using the cockroaches for research purposes, which means he was likely testing fear gas on them. One of the bug crates is broken at the man's feet, suggesting the fear gas being used on the cockroaches leaked out and was so potent that he died from the effects.
Everything in the boat, from the password and dim lighting to the dead man, hints at Scarecrow's plan to flood Gotham with a new version of fear gas. This hidden area effectively built up suspense and anticipation for Scarecrow's return in Batman: Arkham Knight, similar to Warden Sharp's hidden room in Batman: Arkham Asylum. The boat was haunting and confirmed without a doubt that Scarecrow was alive. However, the creepiest messages from Scarecrow in Batman: Arkham were broadcasted over several frequencies and were much more frightening.
Batman: Arkham City Has Coded Messages From Scarecrow
Even though Scarecrow went into the sewers and near the water's edge by choice, he still blamed Batman for the severe injuries he sustained from Killer Croc. During the events of Arkham City, Scarecrow was broadcasting three coded messages to different radio frequencies. Every message was a sequence of numbers, each with its own cipher. One message said, "I will return, Batman," and another could be deciphered to read, "You will pay for what you have done to me." The third message alluded to Scarecrow's plan in Arkham Knight, and it said, "Fear will tear Gotham to shreds."
These hidden messages were the biggest indication that Scarecrow would return as a future villain after Batman: Arkham Asylum. Scarecrow intentionally taunting Batman suggested something terrible was coming and that it would affect the entire city of Gotham. The messages also indicated that Scarecrow was extremely confident about his chances of success, otherwise, he probably wouldn't risk sending direct threats for Batman to decipher. Scarecrow's messages worked with all of the other clues that foreshadowed Arkham Knight's plot. The ominous signs in Batman: Arkham City perfectly set up the sequel by building up anticipation for Scarecrow's return.