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Present Day

2007 - 2012: Desmond Miles

The first five main Assassin's Creed games primarily revolve around the rivalry between two ancient secret societies—the Assassins and the Knights Templar—and their indirect relation to an ancient species pre-dating humanity, referred to within the games as "those who came before", whose society, along with much of Earth's biosphere, was destroyed by a massive solar storm thousands of years before the games. The games' real-world chronological setting begins in the year 2012.

Within the franchise "Abstergo" Industries is a mega-corporation conglomerate with multiple branches, whom secretly is run by the modern-Knights of Templar. The company is the present day main antagonist of the franchise. Abstergo secretly created a device called "Animus", a fictional device that allows its users to "re-live" and experience the memories of their genetic ancestors within their bloodline, this is done through a virtual simulation. Over exposure to the Animus causes the "bleeding effect", which results in giving the user skills and abilities of his ancestors, but also is dangerous for the user as it can break the mind of its user, causing symptoms like dementia, insanity, dissociative identity disorder or brain damage. Abstergo is seeking to discover the location of several historical artifacts, known as the "Pieces of Eden", such artifacts hold great power, and are capable of controlling free will. Abstergo seeks to use them to remove free will and bring humanity into one single unified group, while the Assassins oppose them. In order to find the Pieces of Eden, Abstergo is abducting people whose ancestors are suspected to have had historically confirmed or suspected interactions with such devices, then forcing the kidnapped person into the Animus and searching for clues on their ancestors memories within the Animus.

The main protagonist, Desmond Miles, a bartender who is a descendant of several lines of prominent Assassins; though raised as an Assassin, he left his nomadic family to seek out a more common lifestyle. In Assassin's Creed, he is kidnapped by Abstergo, who is aware of his ancestral lineage. Desmond is forced into the "Animus" and is revealed to be subject 17; many of the sixteen previous subjects died as a result of animus over-exposure. Desmond is later rescued by a small team of modern-day Assassins; and agrees to work with them, continuing to experience the memories of his ancestors to discover the locations of additional Pieces of Eden so they can be recovered before Abstergo can do so. From the bleeding effect, Desmond gains some of the Assassin skills of his predecessors at the cost of living with multiple sets of memories and personalities in his mind.

Within the Animus, Desmond explores the memories of a number of Assassins, including Altaïr Ibn-La'Ahad, an initially disgraced Assassin working to redeem himself during the Third Crusade. Demond also relives as Ezio Auditore da Firenze, an Assassin removing the threats in Italy, Roma and Constantinople during the late 15th and early 16th centuries of the Italian Renaissance. He also rediscovers Ratohnhaké:ton, otherwise known as Connor, a half-Mohawk, half-British Assassin fighting for freedom of his village during the American Revolution.

Throughout these events, Desmond learns of allusions to the prophetic end of the world in 2012 from a former Animus test subject, Subject 16; the event turns out to be a repeat of the disaster which wiped out the ancient civilization, and he finds out that his memories hold the key to Earth's surviving a second solar storm. During his experiences, Desmond is aided by holographic projections of three of the ancient race's rulers: Jupiter, Minerva, and Juno. As December 21 approaches and signs of the solar flare begin to ensue, Desmond opts to release Juno, who is deemed to be a threat to modern day humanity, thus to prevent the end of the world.

2013 - present: Assassin Initiate

After Desmond dies to ensure Earth's survival, his memories, which have survived in cyberspace, are accessed by Abstergo, which hires a new subject to enter the Animus. Samples taken from Desmond Miles' body in the moments after his death have enabled Abstergo Industries to continue to explore his genetic memories using the Animus' newfound cloud computing abilities. In Assassin's Creed IV: Black Flag, the unnamed player character is hired by Abstergo's entertainment division to sift through the memories of Edward Kenway, an eighteenth-century pirate and the grandfather of Ratohnhaké:ton, during the British colonial years. Ostensibly, this is to gather material for an Animus-powered interactive feature film, but in reality, Abstergo and the Templars are searching for the Observatory, a Precursor structure that allows the user to see through the eyes of a subject.

The player is contacted by John, Abstergo Entertainment's information technology manager. John convinces the player that his employer knows more than they are telling, and encourages them to investigate in more detail. He arranges for the player to access the Animus' core, at which point Juno materialises into an incorporeal form. She reveals that although it was necessary to open her temple to avert disaster, the world was not ready for her, and she is unable to affect it or possess the player character as her agents intended. John is unmasked as the reincarnated form of the Sage and attempts to murder the player to cover up the failed attempt at resurrecting Juno, but is killed by Abstergo's security before he can do so. As Roberts, the Sage admits to Kenway that he owes no allegiance to the Assassins or the Templars and instead uses whoever he thinks represents his best chance of achieving his ends.

In Assassin's Creed Unity, the "Initiate" is a player of Helix, a gaming device produced by Abstergo that allows access to many different genetic memories. Bishop provides an internal Abstergo video memo, in which Abstergo describes the capture of a Sage who contains precursor DNA (which is in a triple–rather than a double–helix). Abstergo goes into detail regarding the Phoenix Project, whereby Abstergo hopes to use the Sage to compile a whole precursor genome for unclear purposes. Bishop provides access to another memory segment and directs the new initiate to locate another Sage, whose corpse they hope to recover. The Initiate is once again contacted by Bishop from the Assassin Brotherhood in Assassin's Creed Syndicate, and is tasked with reliving the memories of twin Assassins, Jacob and Evie Frye, to find a Piece of Eden hidden in London. Meanwhile, Rebecca Crane and Shaun Hastings have infiltrated an Abstergo facility and, against orders, decide to spy on a secret Templar meeting. Hacking Isabelle's computer, the Assassins find out the Templars plan to use the Shroud to construct a living Precursor. The recording also shows that Juno is secretly manipulating certain employees within Abstergo from behind the scenes to sabotage the company, and has her own plans for the Shroud.