"I knew we wouldn't last long..." Writes a Templar Agent in a worn, leather book that has some pages falling out. An assassin had got hold of this book before it was completely destroyed in the burning building, and thankfully managed to bring it back in the same condition they had found it.
"After our defeat in Rome, it was only a matter of time. Thankfully, we have managed to regroup and form new alliances. They won't know what's coming in a few years time. Once we have the Apple in our grasp again, nothing can stop us."
For the Assassins, they knew their war had only just begun, and to stop the Templars wrecking the world of the future, they would have to delve into the past.
"But we have hidden the Eagle... No-one knows of its location, but it can be reconstructed if the right person is found."
...
It is five years after the events of Desmond, and the Templars have been defeated. However, they have managed to regroup. You are the new generation of Assassins or Templars, finishing a war that spans hundreds of years.
Enter the Animus.