I believe that Black Flag's modern day parts will actually be you from AC3 multiplayer. Here's why
EN Assassin's Сreed 3 - ALL Abstergo Dev Diaries&Erudito Versions HD10:21

EN Assassin's Сreed 3 - ALL Abstergo Dev Diaries&Erudito Versions HD

Did you notice at the end that the Abstergo Entertainment Lead or more likely new head of Abstergo guy says that they will be contacting you in the future to work for them. This is the whole modern day setting of Black Flag, working for Abstergo Entertainment. Next in the hacked version Erudito says stay strong we will contact you. This is what Ubisoft was probably talking about when they said that you could defect to the Assassins or stay with Abstergo in Black Flag. I'm assuming that by staying with Abstergo you rat out this Erudito guy and if not you will help bring down Abstergo from inside. If this is true then Ubisoft sure has their work cut out for them

To sum it up, in Black Flag you will be a newly hired researcher at Abstergo Entertainment that achieved 100% synergy with the Animus, something that I beliveve you need to relive someone elses memories (i.e William Miles's because his memories were taken when Abstergo captured him). Did you catch something in this video I didn't?  Feel free to leave a comment and we can further unravel the story of Black Flag.

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