If you're trying to capture a lot of territory and stores ect because you think it will impact the plot then stop right now, it has no effect on the story whatsoever.
Getting a high synchronization to unlock hidden memories involves a lot of repetitive crap. And then it turns out those hidden memories are just two minutes of inane soap opera drama.
It's not like the plot could be saved after the AC2 nonsense, and they even managed to make it worse. I shudder to think there are still two games after.
Last good game released by Ubisoft is still Prince of Persia, and I bet that one didn't have a 300+ development team.