The Transylvanian storyline. Having Dracula as a vampire hunter at first seems to be just 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.
It could actually be explained by a misunderstanding from the fans: the Vlad we're seeing is referred to as "the Dragon" and "the founder of the Draculesti (i.e. the Order of the Dragon)"; that would be Vlad II Dracul ("the Dragon"), the father of Vlad III Tepes ("Dracula" is actually Romanian for "Son of the Dragon").
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.
Issue #9 is dotted with references to Alice In Wonderland, with Daimon being highlighted as a stand-in for the Cheshire Cat by the Bees, and the Rabbit Killer being an obvious reference to the White Rabbit - Yuichi actually referring to her by this very name. However, though many other characters have no official tie-in with Wonderland, there are a few clear possibilities: for example, Yuichi and Harumi spend most of their days in a timeless state of objectiveless fun and paranoia, with Harumi being noted for her excitable behaviour and Yuichi easily recognized by his bizarre "space hat"; as such, they're a pretty classic stand-in for the Mad Hatter and the March Hare. For extra fun, take a good look at mercury poisoning (believed to be the origins of the term "Mad as a Hatter") and note that the symptoms include "excessive shyness, confidence loss, and nervousness" - all suffered by Yuichi!
Other stand-ins found in Tokyo may include the following: Gozen for the Duchess - both being aggressive matriarchal figures with a tendency to ramble on about morals and morality, both employing an equally aggressive cook (Akashi) and a set of underlings with a distinct lack of attention to detail (the Duchess's footman paying little attention to visitors, the Jingu Clan failing to notice the fact that they were borrowing vehicles from a death cult). Sarah is a stand-in for Alice - though admittedly, Sarah's a bit more ragged than the original Alice, having been subjected to a maddening Mind Rape while trapped at the bottom of Tokyo's subway system (for all intents and purposes, the Rabbit-Hole of Tokyo) . Finally, what with the repeated motif of flipping Tarot cards utilized by the lore entry on the Orochi Group, the Queen of Hearts can only be Lilith, with Samael/Samuel Chandra naturally representing the King of Hearts. From here, it's also possible John is the Knave of Hearts, especially given that he's deathly afraid of being caught and punished by Lilith.
During the "Headhunter" sidequest in Egypt, only one of the Marya recruits is still alive when you find him. And while you're doing "The Traitor" quest, if you pay attention, the house the traitor was based in is the same one the only surviving recruit lived in, and that same recruit shows up at the end of the mission as the Aten informant. Which explains why all the other recruits are dead or Filth-infected.
When reading the Buzzing and the Black Signal lore from Issue #9 you will notice that the Buzzing often ending their message in sudden mess of unintelligible characters while the Black Signal's lore opens with the hiss of radio static. It makes sense when you realize John is literally hijacking the Buzzing's frequency.
A little bit meta: many players were annoyed by ice-cream koans and fortune-cookies babbles in Dragon debriefings, which made their mysteries and inscrutability sort of Informed Attribute. Then we learn that Bong Cha was deemed totally incompetent, memory-wiped and replaced with Daimon Kiyota - the Dragon admitted and corrected their flaw In-Universe.
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.
In one lore entry, the bees say that the Third Age ended "under tentacular skies," so when Lilith says the Third Age ended when a barely woken Dreamer "strangled the world," it might not entirely be a metaphor. The end of the Third Age must've been far more horrific than a 'normal' cataclysm.
The Dragon Lore tells of some of the things they were doing over the years, one account is of how they were injecting rats with the black plague during the dark ages. Now this is eerie enough but goes with the notion of seemingly chaotic acts all fitting into social engineering, gee a secret society is willing to kill masses, shocker... But then in The Ankh, Dr. Klein makes reference to his experiments being "The most important Filth event since the Black Plague."... Which means... The Dragon were ACTUALLY SPREADING SOUL DEVOURING, REALITY CONSUMING, BODY POSSESSING, LITERAL NIGHTMARE FUEL! Whether they knew what it was at the time, to say nothing of how trust worthy Klein is may offer them some level pardon but god damn!
In the lore about the Arthropods the Bees confirm that the Locust are the ones described in the Exodus. Biblical Horror, yeah. But here is the real question: If the locust were like that, just how bad were the other Nine?!
There is a Guardian of Gaia for each type of golem, except for flesh. We also know that they manifest from big quantities of their elements, like the Ice Guardian manifesting from a lake or the Sand Guardian from a desert. Also, they are bigger that most buildings. Taking that into account, where a Flesh Guardian would manifest? In the place of a genocide? From the corpses of the victims of a natural disaster? Or it's even possible that some people, maybe an entire town because of the hundreds of corpses needed to manifest this kind of monster, would be fused together while they are still ALIVE?! After all, if the Bees are not lying like the Black Signal says, the Guardians lack any morality or restraint and there is a long list of populations across history and before that just disappeared one day without leaving any clue about how or where these people go...
While moving towards Times Square in the New York raid, it is possible to see Spider Guardians crawling down the walls outside the parking garage. However, in no point during this raid does the raid group fight these creatures and they are never mentioned - this means that there is now bunch of filthy spider abominations loose in New York.
Säid is able to function perfectly fine as a mummified corpse... however, Egyptians believed, incorrectly, that the brain was an inconsequential organ, and the heart was the seat of bodily function. Mummification in Egypt involved the brain being extracted through the nose, among other unpleasant processes. While the stomach, liver, intestines and lungs were all sealed in canopic jars to be buried with the mummy and the heart was left in the body, the brain was thrown away. The four canopic organs were all buried with them to be symbolically present in the afterlife, so that can be explained away with magic, but the brain held no significance in Egyptian mummification. How can Säid normally function?
Body doesn't matter. How can Said see anything given that, according to the lore entries, he has no eyes? How can he move at all given that his muscles are just desiccated beef jerky by now? Nothing in Said's body should function at this point, and the only reason he's up and about is due to a freak accident of Anima: he's not a functioning organism in any biological sense of the word; he's a lump of embalmed meat being animated and piloted by his soul. In fact, it's for this very reason that Said scoffs at threats from Tanis: he has no biological weaknesses she can exploit - no Removing the Head or Destroying the Brain, apparently.