Finished the main story? Brilliant, brilliant game. More questions than answers...
About the ending...
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Lucy is killed by Ezio. However, when you're in Memory Sequence 5, when you get out of the Animus and explore outside of the villa, there is a blood trail. Theory as to what this could be is, Abstergo agents knew where they were, abducted Lucy (she put up a fight, thus the blood trail) and replaced her with a decoy. At the end of the game, Ezio is forced to kill Lucy because she isn't Lucy to begin with.
By the way, AC:B ends the story of Ezio. His work is done. According to the dev team, the next (and final) game "Assassin's Creed III" we will be playing an entirely new character. Rumor has it either USSR or ancient Rome (I doubt the latter).
They should let us play the final game in modern setting entirely! Imagine dodging cars and gunmen, leaping onto modern sky scrappers and shiny buildings. The ability to escape using trains and tagging along cars. Or even ability to drive cars. This would be amazing.
I doubt AC3 will be this year, perhaps a DLC will be available that hints at the next game.
Oh well, I haven't found all of the Romulus lair and the strange coordinates. I left MP for over a month and will be back...