Assassin's Creed II begins immediately after the events of the first game in 2012; Desmond Miles is still trapped by Abstergo Industries (the modern-day face of the Knights Templar) after being forced to use the Animus device to revisit genetic memories of the Assassin Altaïr Ibn-La'Ahad, and has discovered prophetic warnings from Subject 16 (a previous captive) describing the end of the world. He is soon rescued by Lucy Stillman, a mole for the Assassins within Abstergo, who takes him to meet two other Assassins, historian Shaun Hastings and computer expert Rebecca Crane. They request that Desmond use their version of the Animus, dubbed the Animus 2.0, to relive memories of another Assassin, Ezio Auditore da Firenze, to train Desmond in the ways of the Assassins through the "Bleeding Effect" of the Animus. During his exposure, Desmond finds himself briefly struck by a puzzling memory of Altaïr and his lover, a former Templar named Maria Thorpe, who became pregnant with his child. It is also revealed that apart from training Desmond as an Assassin, the Assassins also wish to find out more information about the foretold "Vault". Desmond also finds various glyphs left by Subject 16 in the Animus, which, when decoded and assembled, form a brief video of a man and woman, "Adam" and "Eve", running through a futuristic setting called "Eden". The video ends with the binary for "EDEN" (00100101 00100100 00100101 00101110).
Ezio's memories begin during the Renaissance in the 15th century, where his family is ensnared in a political plot, and his father and brothers are hanged. This story is told in the 35 minute prequel short, Lineage.
Ezio, following his father Giovanni's last advice, finds his father's Assassin tools, and flees the city with his mother and sister to the safety of his uncle Mario's villa in the countryside. Mario assists Ezio in discovering the people behind the conspiracy, the search leading Ezio from Florence, to San Gimignano, Forlì, Venice and eventually to Rome. As he identifies and assassinates more and more political figures, Ezio also gains several allies, including Niccolò Machiavelli and Leonardo da Vinci, the latter of whom helps Ezio improve his equipment using schematics found in Altaïr's Codex pages. Eventually, Ezio identifies the mastermind of the plot: the Spaniard Rodrigo Borgia, who ultimately sought to bring down the Medici family in Florence with the help of the Pazzi family and the Doge of Venice. Ezio finds Borgia in possession of the Apple—a similar Piece of Eden that Altaïr had recovered centuries ago—and learns that Borgia believes himself to be "the Prophet" that will lead the Templars to a fabled "Vault". Ezio is able to confront Borgia with the help of his allies and recover the Apple, but Borgia flees before he can be killed. Ezio's allies reveal they are all Assassins, and see Ezio as their Prophet, allowing him to join their ranks.
After this memory, the modern Assassins discover that several years of Ezio's memories are inaccessible from the Animus. Desmond can only revisit those starting in 1499, where Ezio and the Assassins plan to attack Borgia (now Pope Alexander VI) at Vatican City. Ezio corners Borgia and strikes him down, but refuses to kill him, as he knows that it will not bring back his family.[18] Ezio uses the Apple and the Papal cross (which is also a Piece of Eden called the Staff), and discovers the entrance to the Vault. Inside, he is astounded when a holographic figure, calling herself Minerva, appears. Speaking directly to Desmond and those monitoring him in 2012, she explains that she was part of a far more advanced society that initially co-existed along with the early humans on Earth before they faced each other in war. A global catastrophe occurred that nearly wiped out both sides, and the survivors joined together to construct "temples" across the Earth to allow humans to prevent a similar catastrophe in the future. Before the hologram disappears, she warns Desmond—by name—that "the rest is up to you".
Shortly after recovering this memory, Desmond and the others are forced to flee with the Animus 2.0 from their location as Abstergo troops surround it. There, they encounter Warren Vidic, who flees when Desmond and Lucy deal with the troops. As the team heads towards a new safehouse, Lucy explains that there are newly-discovered weaknesses in the Earth's magnetic field; a solar flare striking this weakness would cause a similar level of global destruction as described by Minerva. Desmond resolves to help the Assassins find these temples, and prepares to re-enter the Animus, knowing that Ezio may hold the answers they seek.
