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The Transylvanian storyline having Dracula as a vampire hunter at first seems to be a Take That against Bram Stoker, but remember that Vlad Tepes III's nickname is The Impaler having him as a Vampire hunter instead of the Father of all Vampires makes sense after all why would a Vampire use impalement as a method of execution. It may also count when you consider Vlad's local reputation in Romania where he's a national hero.
The Solomon Island Storyline. The reason taking Excalibur caused the Filth to invade? The light of it was keeping it at bay. Without anything to restrain it it grew to the point where it overwhelmed the other wards.
The reason why the manager of The Dream Palace in Kaidan wears a sexy sailor outfit? Her employers are the Phoenicians and the Dream Palace is their base of operations in Tokyo.
The final mission of issue 10 shows how John was chosen to be carrier of the Filth bomb and what happened after. The fridge horror comes in you realize that John was not the first choice and that it could have been Yuichi that it all happened to.