In an interview with Eurogamer, a director from Assassin's Creed 4: Black Flag has elaborated on the modern-day section of the game and a feature that will use this section to connect your game with those of your friends. Ash Ismael was quick to reassure Eurogamer and its readers both that the game will have a multiplayer mode and that the separate multiplayer features for the single-player part of the game will be completely optional.
The connectivity is based on the fact that – unlike in the previous games (on home consoles) in the series – the player doesn't play as Desmond but as herself. You are a research analyst at Abstergo Entertainment, the company that represents the Templar antagonists to Desmond in the modern day in those other games. You're researching the life of the protagonist of the historical sections of the game: the pirate Edward Kenway. As part of that, you will have coworkers who are also conducting research, and these coworkers will be represented by other players:
“The coworkers with you – we want you to feel that your friends are co-workers. So other people playing Black Flag are also research analysts. So when they can find stuff in the world, they can share it with you. When they do research, and when you're doing research, you can share that information and you get a boost for it.”
So it doesn't quite sound as though you'll be able to walk around a virtual Abstergo lab with your friends' avatars, but it does show that Ubisoft is keen to improve the modern-day sections and make them more interesting. The game will even feature something for fans of Desmond, with side content that “kind of fleshes out” a little more of his story.