BEFORE THAT HOWEVER: I want to say that this Fanboy Theory will be SPOILING the 100% ending to Batman Arkham Knight. If you haven't beaten the game, get to it!
Theory A: Batman(without Bruce Wayne)
This actually has been done before in Batman RIP, written by the king of mind-benders Grant Morrison. In the story, he recreated the old character of the Batman of Zur-En-Arrh, reimagining him as a Batman "when you take Bruce out of the equation." This equates to him torturing and even KILLING people to get to their bosses. Does that sound like the Batman we've played as for four games?!
So how do these two things connect? As seen in the image above, he turned into a monster...or is it that's what he wants you to think? Batman might have taken what Fear Toxin is left from Scarecrow and now uses it for his own needs. "But that stuff is too dangerous and deadly," you might be saying in your head. You are correct....its too dangerous for Bruce....but not for Batman.
Theory B: Azrael or Red Hood
As I said in the last paragraph, the fear toxin would be much to dangerous for the Batman we played as to use on common thugs. It was lethal in the sense that it caused the person to either go mad or kill themselves. Despite that, there are a few heroes who would use it if they had a chance to.
As we saw in the game, Jason Todd put down his mantle of the Arkham Knight and became his own vigilante. That being said, he is the only Bat-Family member left patrolling as Dick is in Bludhaven and Robin got married to Oracle. With the Cowl needing someone else, and he might feel guilt that HE lead to the unmasking of Batman, it would make logical sense that not only would he take up the role, but combine it with his own morals.
However the main candidate for the Bat that I think of is Azrael, whose order thinks that he should kill every criminal on the street in the name of god, using whatever weapon is at his disposal. With the fear toxin, he'll be able to become a scarier version of Batman, which he incidentally did when his back was broken in the comics. I'm not saying that the Azrael side mission left it open for him to become a protector of Gotham, but I am saying that the protocol was called Knightfall.
Now before we get to the final theory, I want to warn you its a little crazy...and I need to ask a single question... If the Batman at the end is one of the theories above, and their using fear toxin to create that image...where would it be taken in? There are now pipes or grates in the alley, and the closest thing to a gas is the rain-esque steam which is white where the toxin is brown...so how are the thugs seeing Batman like that?
Theory C: The Spectre(kinda)
What if Bruce did want to kill himself. He has no reason to go on at this point, especially with his identity being revealed and putting all his friends and family in danger. He entered the house, ready to die, but was brought back in secret by God. Gotham will always need a Batman to protect it, and rather than let the soul be at rest, he is chosen to be it's spirit of vengeance. Granted the new supernatural powers, Bruce will now forever protect Gotham from crime as the true Batman.
How can Spectre level phenomena exist in a world that seems pretty science driven? There has been no magic to imply the supernatural existing! WRONG! Grundy and his curse exist in this world, Zatanna exists in this world, THE FRIGGIN LAZARUS PITS EXIST IN THIS WORLD! This world is supernatural, even if the games creators never put the spotlight on it.
There is no explanation towards the shadowy Batman, especially now when you think about the fact there was no seen dispersal of the fear toxin. To quote the world's greatest detective, "How often have I said to you that when you have eliminated the impossible, whatever remains, however improbable, must be the truth?"
Thats it for the Arkham Knight Fanboy theory! What did you think that shadowy batman was? Leave a comment and i'll see you all next time!