"Croatoan", uttered by Dylan in his conversation with Beka towards the end when he decides to go after Stark, is a reference to the Roanoke Colony of 1587. Dylan references the theory that "the colonists never left." In this theory, the colonists dismantled the settlement and moved to be closer to Native American allies on the island known as Croatoan, eventually integrating into the local populace, thus having "never left." This appears to have been the belief of Governor White when he returned to the colony in 1590, after having left in 1587 in order to seek supplies for the starving colony, and found the word carved into a post at the settlement.
"Twilight of the Idols" comes from an 1888 book by Friedrich Nietzsche "Götzen-Dämmerung" with the subtitle "How to philosophies with a Hammer". It further ties into "Götterdämmerung", the conclusion of Wagner's Ring cycle, and the Teutonic equivalent of the Norse "Ragnarok", the apocalyptic battle in which almost all the gods perish.
The motto of the High Guard Argosy Special Operations is una salus victis (nullam sperare salutem) (The only safety for the conquered is to hope for no safety.).