There have been mentions of an alien race, with interest in alien artifacts, usually referred to as "the unknowable Tsab", and one of their captured devices is called Bah'ri Di ß".
Mythos-related tomes that Gendo has acquired include several HP Lovecraft stories, The Tales of the Black Freighter, and "the full product of that unknowing seer, Nagura Tanigawa", which explains the relationship between Azathoth and Nyarlathotep.
The Director of Special Services is called Khoury, just as the head of the Achtzig Group is Dr Calvin Sylveste. That's a thing of such profound technohorror that it's traumatic to think of it.
Dr Simon Tam works for the Ashcroft Foundation, who just happen to run a R1VER project.
The Reavers get a Shout-Out when describing the Rapine Storm. "Words were not necessary to explain what that meant. The human Disciples, if the term could apply to those degenerates, would rape you to death, eat you and wear your skin as clothing. These actions could even be re-arranged."
Gladys Chell was transferred to Project Achtzig. Earth Scorpion jokingly claimed that Shodan von Braun is another employee.
"The latter sentence, meanwhile, was as demonstrably as false as Cake's hypothesis on the nature of existence." SoCake is a lie?
NEGN/NEGA doctrine is to enter "autistic mode" when engaging Migou forces, and the NEGN/NEGA deploy "Chalybion" helicopter drones with tail-mounted guns. These are nicknamed "Jigabaki" by the Loyalist Nazzardi..