Some civilians are Abstergo employees. Abstergo is the company featured in the Assassin's Creed series.
In Assassin's Creed IV: Black Flag (2013), you can hack into computer messages. One of them shows Blume explaining ctOS to Abstergo employees.
In an interview with Ubisoft Creative Director Justin Morin, he revealed that Aiden's character was created based on a person who had saved him from a robbery in his hometown of Chicago. When Morin asked the man his name, he replied "Archer." This created Aiden's name. A was for Archer and Pearce represented an arrow piercing a target.
The dead body in the lighthouse you will find completing the Serial Killer side mission is a reference to the TV show Dexter (2006).
Raymond "T-Bone" Kenney is the only playable character besides Aiden Pearce.