Brotherhood is the 3rd Assassin’s Creed video game and the 2nd one that involves Ezio’s life as an assassin. Unlike the 2nd game, this one begins exactly where the 2nd ended. Ezio Auditore da Firenze, a young assassin is in an ancient vault beneath Vatican and he is confused after hearing Minerva‘s message. Right after the message ends, Mario Auditore, Ezio’s uncle, walks into the chamber and tells Ezio that they need to get away before the guards catch them. The two assassins manage to escape and together they return to their home in Monteriggioni with the Apple of Eden. Ezio is now relieved and glad that he touched his goal and he is ready to leave his life as an assassin behind. Back in Monteriggioni he meets once again with Caterina Sforza.
The next day, a surprise attack is launched against Monteriggioni. Apparently, the attack was led by Cesare Borgia, Rodrigo‘s son. The assassin’s cannot stand the Templar’s force and Monteriggioni falls; Mario Auditore is killed by Cesare, the Apple is taken by him and Ezio is shot in his shoulder. Luckily, Ezio and the rest of his family escape to Rome, the main city of the Templar Order and the place where they were exercising their power. In Rome, Ezio meets with Niccolo Machiavelli. who reproaches Ezio for letting Rodrigo alive. While walking in Rome, they see what the corruption of the Templar was doing to the city and that the Assassin’s Order was decaying and loosing power. Ezio encouraged Niccolo and starts rebuilding the Brotherhood.
For the next 4 years, Ezio is rebuilding the Order; he recruits new and young assassins and he is trying to break the Templars by killing key members of their order and tries to restore Rome to its former glory. Because they were losing ground, Cesare asks his father for more money, power and eventually the Apple itself. Rodrigo notices his son’s thirst for power and attempts to poison him but he is killed by Cesare instead. Witnessing the whole scene and learning about the whereabouts of the Apple, Ezio finds the artifact inside St Peter Basilica. Ezio uses the Apple to stop Cesare’s influence. Eventually, the Templar leader is arrested by the forces of the new Pope. Cesare escapes the prison and runs in Spain. While he is sieging a city, Ezio finds him on the battlefield and throws him down from a wall, leaving him to die. Ezio takes the Apple and hides it in an another temple underneath Santa Maria in Aracoeli.
Using the coordinated from Ezio’s memories, Desmond, Lucy and the other assassin go to find the Apple. Inside the temple, the Image of Juno appears but she is visible and audible only to Desmond; she looked like she was part of the same civilization that Minerva was part of. Juno is saying that humans are ignorant and innocent and they were not build to be wise and that they were given only the basics senses. She also stated “We should have left you as you are!”. As soon as Desmond touches the Apple, the time freezes around him but he can still move or speak. Juno tells Desmond that he is a descendant from her race and their enemy and that a woman should accompany him through “the gate” but the woman is not there. She takes control over Desmond’s body and makes him stab Lucy, killing her. The game ends with Desmond falling into a coma. Right after, his companions take him back to their base and put him back into the Animus.