Fortunately, Desmond was rescued by Lucy, the researcher who had navigated Desmond into the Animus in Assassin's Creed 1. She was, in fact, a member of the Assassin Order.
To counter the modern templar knights, he had to enter another Animus and find his path forward by tapping into the memories of another ancestor named Ezio. Through the Bleeding Effect, Desmond himself was gradually becoming a real assassin.
Meanwhile, the game told the players that the modern templar knights had found out the assassins' hideout and forced them to move to another place.
Animus 2.0 was the updated version developed by an assassin engineer named Rebecca Crane. With the fragmental blueprint delivered secretly to them by Lucy Stillman, who was an assassin spy in the Roman branch of the Templar Order, Rebecca made this new version in the hideout of the Brotherhood.
