As far as I know, it's supposed to be a trilogy. So you can be sure they continue the storyline they build with the first game.
If you read the e-mail in the conference room towards the end of the game, there was a part about the holy grail. Basically Abstergo thinks it doesn't exist, which could lead to this plotline:
First game deals with the pieces of Eden and how they fell in the hands of the brotherhood (in present day). Second game could deal with the Assassins tracking down the grail and how it falls in their hands in present day. Then the third game could be set in present day and how the Assassins try to stop the Brotherhood from launching that satelite, or possibly neutralising it after it launches. Desmond, now with the full skillset of his ancestors, could be the main character in the last game. After all, Desmond already obtained that "eagle-vision" at the end of the first game.
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Contritium praecedit superbia.
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