A wierd theory about the ambiguous Knightfall ending, more of a proposal, but I sort of think that the Arkham games are based in Earth-43(One of the multiverse, look it up if need be). I say this due to the fact that in both universes, the joker was killed. In the Earth 43 comics(I'll clarify why this is important momentarily) he was killed by Batman snapping his neck, and drinking his blood. In the games, however, it was simply blood poisoning. About that blood drinking thing, there is a version of Batman where he became a vampire, killed Joker and drank his blood, only to request Alfred to kill him(And this will be important as well), but he returns as a monster actually quite similar to that end shot in the Protocol ending, and it is sometimes referred to as,"Nightmare Batman". In the concept art of the game, it is seen that this end shot is actually referred to by the exact same name. To implore more on why this might be true, think about what the Joker did to Batman back in City, being that he injected Batman with his own blood. Now, call me mistaken, but Bruce almost becomes a rampaging "monster" when he gets a whiff of the fear gas, a nimble body with the mind of a lunatic, the Joker. In this instance, Joker almost breaks the Dark Knight, but the events that conspired may have proceeded to indeed make him lose his mind. In Earth 43(I'll be calling this the Vampire Batman comics from here on) Joker does break the Bat.(Even though Bruce was the one that broke the Joker...get it?)Batman(dubbed Vampire Batman from here out) , horrified at his actions, proceeded to request Alfred to kill him with a stake, which actually only sent him into a coma. or so to speak, locked away from the real world. It is mentioned that Bruce intends on locking himself away in Arkham Knight once the night is over with, to make sure he never becomes a monster and hurts the people he once protected. This sounds a bit familiar, doesn't it? In the Vampire Batman comics, he is freed by Alfred, who was hoping that he would save Gotham, but instead starts killing his enemies. With this, though, it was because of bloodthirst, I understand, but still. In the games, it is very possible that the Knightfall protocol was to ensure noone would come looking for him once he locked himself away from humanity. Is it not possible as well that the Joker persona inside of him could very well be freed from the mental prison "Bats" created for him, while Bruce is locked away in a prison of his own, eventually freed in hopes he would ensure Gotham's safety? In conclusion, I theorize that the Arkham games were, in a way, a more "realistic" approach to the Earth 43 comics, or the Vampire Batman approach. With that, I'm open for thoughts on what may or may not be wrong with that theory, so do give any critique if you feel the need!