- "男の選んだ道ではなかった。それはまさに宿命だった。復習の成就は容易かと思われた。闇の奥深くに身を潜め、罪多き者達に死の制裁を加え。そして、風のごとく姿を消す。そこにいかの大きな陰謀が渦巻こうと、その手が総てを終焉に導く。男の名はエツィオ・アウディトーレ・ダ・フィレンツェ。 宿命に生きる。生きてこそアサシン。"
- ―ナレーション Assassin's Creed II ローンチトレイター
The game begins with Desmond giving a brief monologue about the events of the first game and his current predicament. A few hours after the events of Assassin's Creed, in the year 2012, Desmond Miles touches upon how he was held prisoner by the modern-day Knights Templar, Abstergo Industries, and was being forced to relive the genetic memories of his ancestor, Altaïr Ibn-La'Ahad, in order to aid Abstergo in discovering the location of artifacts known collectively as the "Pieces of Eden".
Due to the "Bleeding Effect", Desmond has gained "Eagle Vision," enabling him to see a variety of messages and symbols written in blood on his bedroom wall by its former occupant, known only as "Subject 16". While staring at the message, former employee and researcher of Abstergo, Lucy Stillman, arrives, covered in blood, and frees Desmond from the room. He then re-enters the Animus briefly and watches the birth of Ezio Auditore da Firenze, as she makes a copy of the files located within the machine. The two then escape after a brief scuffle with the company's security guards and arrive at a warehouse in which Lucy and two other modern day Assassins, Shaun Hastings and Rebecca Crane, have set up their own base of operations, complete with their own version of an Animus.
Desmond is asked by Lucy to enter their version of the Animus and relive the genetic memory of his ancestor Ezio Auditore da Firenze, in order to continue the search for the remaining Pieces of Eden before Abstergo locates them. Due to the number in the Assassin Order seriously dwindling, Lucy informs Desmond that she intends to train Desmond in the various skills needed to become an Assassin by exploiting the Bleeding Effect and having Desmond absorb Ezio's abilities.
Ezio, living in Italy during the Renaissance, is approximately 17 when he discovers that his family was betrayed by a close friend of his father's in the midst of a political coup d'état. Ezio's father's final instructions lead him to a hidden room in the family home with a chest containing the clothing and weapons of an Assassin. Ezio is ultimately unable to save his two brothers and father from the betrayer and all three are falsely convicted of treason and hanged.
After evacuating their home and sharing a brief accommodation with the family's housemaid's sister, who teaches Ezio some survival techniques, he brings his panicked sister and muted mother to the family's countryside villa, where they are given shelter by Ezio's uncle Mario, who begins training Ezio to become an Assassin. Mario also provides information and leads on the conspirators involved in his family's betrayal, which becomes a trail stretching from Florence to San Gimignano, Forlì, Venice, and eventually the Vatican.
During his travels, Ezio befriends several citizens of Italy who aid him in his pursuit for revenge, including a young Leonardo da Vinci, who translates and decodes pages of Altaïr's Codex, enabling Ezio to gain new weapons and assassination skills. Ezio begins slowly locating and assassinating the conspirators involved, and is ultimately able to identify Rodrigo Borgia as the overall leader, whose main goal is to bring down the Medici family and take control of various portions of Italy.
Ezio tracks Rodrigo to Venice and discovers that he has obtained a Piece of Eden known as the "Apple," a similar artifact to one that Altaïr possessed almost three centuries prior. Rodrigo has been researching the knowledge surrounding the Pieces of Eden extensively and believes himself to be a prophet named in the documentation of the artifacts, which would ultimately lead him and other Templars to a location known as "The Vault", which is believed to contain powerful information and more Pieces of Eden.
Ezio and Rodrigo duel and when Ezio gains the upper hand, guards appear and begin to move the fight into the favor of Rodrigo. The allies that Ezio has made over the years arrive shortly after and they defeat Rodrigo, who flees for fear of his life, leaving the Apple behind. These allies and friends of Ezio finally reveal their common trait – that they are all members of the Assassins, including the great Niccolò Machiavelli. They induct Ezio into the Order, informing him that they believe him to be the actual prophet who will lead the Assassins, not the Templars, to the Vault.
Desmond takes short breaks from the Animus, and during one he is tested by Lucy to see if the Bleeding Effect has been working. Desmond is able to demonstrate all of Ezio's skills, indicating that he has absorbed years worth of abilities in only a matter of hours. During this break, however, Desmond suffers a strange hallucination which returns him to the body of Altaïr in Acre. During the memory, Altaïr makes love to Maria Thorpe, an ex-Templar, and Desmond is confused to find that after Altaïr leaves, the memory stays behind with Maria.
Throughout the genetic memories as Ezio, Desmond discovers multiple glyphs placed on various landmarks that are only visible to someone using the Animus. The glyphs are found to be the same ones drawn on Desmond's bedroom wall in Abstergo, and analysis reveals that they contain computer code, hidden within the Animus. It is ultimately discovered that Subject 16 hacked the Animus and placed the glyphs within the memories himself, which were carried over to the new Animus when Lucy loaded the information she had recovered at Abstergo. Each glyph contained a great number of historical artworks, photographs, and messages, past and present, implicating a great number of prominent events and figures with the Templars and Pieces of Eden. Each also contained a puzzle of some sort which, when solved, contained clips of a larger video. The clips, however, are short and out of sequence. After locating and solving all twenty glyphs, a video is revealed.
The video begins with the Abstergo logo shown above the title, "Subject 16, Session 12, Classified Date B.C.E." The video follows a man and woman, who call each other by the names of "Adam" and "Eve", running through a strangely modern and futuristic world, apparently being chased by someone or something. They pass through a complex where workers are busy building more Pieces of Eden and climb to the roof. Eve holds up the Apple and the video suddenly ends with a flash of binary code that translates to "Eden".
Desmond returns to the Animus and the team finds that many of the following memories are corrupted. They are able to begin again but only years after the fight between the Assassins and Rodrigo. The memories restart in 1499 and the team discovers that the latter gained influence and power in the Catholic Church, ultimately becoming Pope Alexander VI. Ezio and his allies have searched long and hard and collected all thirty pages of the Codex, discovering through it that the Vault lies in Rome, specifically underneath the Vatican. They realize that the Papal Staff is another Piece of Eden and Rodrigo is hoping to use it to achieve access to the Vault.
Ezio travels to the Vatican and attempts to assassinate Rodrigo, who uses the Staff against Ezio, who retaliates with the Apple. During the ensuing battle, Ezio is stabbed and Rodrigo escapes with both Pieces of Eden. Ezio then chases after him and finds Rodrigo trying to open the Vault in vain. The two fight once more and Rodrigo finally falls. However, Ezio refuses to kill him, insisting he has killed enough in his life and the continued deaths will not reverse the fate of his family.
Ezio proves himself to be the Prophet when in his hands, the Apple and Staff open the Vault. Inside the Vault, he finds not Pieces of Eden but an empty room and a holographic figure named Minerva. She claims that she brought Ezio to her so that almost six hundred years later, Desmond and his allies would hear her words through the Animus.
Minerva explains that she and her race were part of an advanced society that settled on Earth before a celestial event destroyed most of the life on Earth. Before the disaster that befell them, the members of her species created humans and used them as a race for workforce. However, humanity rebelled against their creators and initated a long-spanning war. Ultimately, the humans seemingly won, but then the catastrophe occurred, wiping out many humans and the precursor race. Of those remaining, the two specied worked to recreate the world, before the advanced race sealed themselves in temples around the world, hoping to prevent the same disaster that had destroyed most of their kind from happening once again. As Minerva finishes, she speaks to Desmond by name and informs him that she has done all she needs to and that the rest remains up to him and his allies.
The memory ends and Desmond awakens in the present to find that Abstergo has located and begun attacking the Assassins as Shaun and Rebecca pull him out of the Animus. Desmond is given a Hidden Blade by Lucy and the two run downstairs to stop the guards as Shaun and Rebecca pack up their equipment. With the skills he absorbed from Ezio, Desmond is able to dispatch the forces that have been sent against them and he discovers Warren Vidic standing in the back of a truck. He sarcastically tells Desmond to enjoy his temporary victory and the truck drives away. From there, Shaun and Rebecca finish gathering the equipment and Lucy assures Desmond that Vidic will get what he deserves.
The group vacates the hideout and attempts to find a new safehouse, where, according to Lucy, they should be safe for some time. As they drive, Lucy prepares to review the tapes of Desmond's latest session, noting how the situation has escalated dramatically and how Minerva's words proved everything she was afraid of. She theorizes that Minerva was discussing the Earth's geomagnetic reversal, which could have detrimental effects on the planet. Rebecca prepares the Animus for Desmond to re-enter as Lucy speculates there may be more to discover in his memories.
- エツィオ・アウディトーレ・ダ・フィレンツェ 声:関智一
- ジョヴァンニ・アウディトーレ 声:内田直哉
- フェデリコ・アウディトーレ 声:堀川仁
- クラウディア・アウディトーレ 声:桑島法子
- マリオ・アウディトーレ 声:大塚明夫
- レオナルド・ダ・ヴィンチ 声:森川智之
- ロレンツォ・デ・メディチ 声:浅沼晋太郎
- パオラ 声:岡本麻弥
- カテリーナ・スフォルツァ 声:名塚佳織
- ローザ 声:小林ゆう
- アントニオ 声:小杉十郎太
- ニッコロ・マキャヴェリ 声:白熊寛嗣
- フランチェスコ・デ・パッツィ 声:青山穣
- ヴィエリ・デ・パッツィ 声:下山吉光
- ロドリゴ・ボルジア 声:山路和弘
- ルドヴィコ・オルシ 声:ふみいち
- チェッコ・オルシ 声:えどさん
- クリスティーナ・ヴェスプッチ 声:平野綾
- ショーン・ヘイスティングス 声:飛田展男
- レベッカ・クレイン 声:渡辺明乃
- 被験体16号 声:浅沼晋太郎
- デズモンド・マイルズ 声:東地宏樹
- ルーシー・スティルマン 声:園崎未恵
- ウォーレン・ヴィディック 声:多田野曜平