Ubisoft game developers have stated "Assassin's Creed IV: Black Flag" is their way of saying goodbye to Desmond Miles in the series.
Warning: MAJOR SPOILERS UP AHEAD
At the end of "Assassin's Creed III", Miles is convinced by Juno that in order to save the world from repeating history, he must sacrifice his life. He touches a device that kills him and Juno's plot to change the course of the world has succeeded, for better or worse (you can't really tell what she's up to at this point).
"Assassin's Creed 4" picks up where the story left off, as you take on the role of a new DNA researcher for Abstergo Entertainment, a company that you eventually find out is run by present-day Templars. Miles' friends and fellow Assassins, Rebecca Crane, Sean Hastings and possibly his father William Miles, are attempting to gather information by infiltrating the company through hacker and your co-worker John.
Once John teaches you how to hack into computers, you will uncover files detailing what happened to Miles. While the information about Miles isn't exactly detailed, you do receive confirmation that he is dead in Sample 17 hacked files.
"After the events at the end of Assassin's Creed 3, wherein Desmond sacrificed himself to prevent a cataclysmic event from destroying most of humanity, Abstergo research teams found and recovered his body," IGN reported. "After the following autopsy, Abstergo Entertainment utilized Miles's DNA to create the Sample 17 project for their Animus entertainment system, starting with the Edward Kenway memories that players experience in Black Flag."
Along with Abstergo's paperwork about Sample 17, the Templar company created a video about Miles, showing you images of his dead body. As for why Rebecca and Shaun were looking into Absertgo employee Olivier or if they were behind his disappearance, "Assassin's Creed 4" never answered those questions.
In fact, the end of "Assassin's Creed 4" leaves you with more questions than it gives you answers. For example, what is Juno's plan for the future? What's going on in the present-day world of the Templar and Assassins? WHERE IS OLIVIER AND WHY IS HE IMPORTANT?
What do you think is going on in the present day "Assassin's Creed"? Leave your theory in the comments section below.
Warning: video contains "Assassin's Creed 4" spoilers!