Operating since at least 1980, and led by Dr. Warren Vidic – with Lucy Stillman joining some time prior to 2010 – the Animus Project was one of the most important Abstergo initiatives in their history.
The project mainly included the kidnapping of Assassins or their descendants via the Department of Lineage Discovery and Acquisition, the exploration of said captives' genetic memories, and the acquisition of Pieces of Eden.
Subject 1 was a male individual with an ancestral connection to Aveline de Grandpré, performing Animus sessions around late 1980 until January 1981. After reliving the lives of other ancestors, Subject 1 was assigned to relive Aveline's memories in 18th century New Orleans. However, his connection with the Animus readily destabilized and he suffered a seizure, resulting in his death.
Following the failure of Subject 1 in early 1981, Vidic personally volunteered himself as the next Animus subject to keep the project running. He took a four-hour Animus session, reliving the life of an ancestor in 18th century Hungary and of one of Joan of Arc's executioners in 1431.
In 1983, Subject 4 (codenamed "Daniel Cross") – an 11-year old orphaned boy – was delivered to Warren Vidic by Lineage Discovery and Acquisition. From then on, Daniel was used in the Animus for his genetic memory to be explored, but also for his brain to be experimented upon using a replicated Piece of Eden.
After the experiments were finished, Daniel was released onto the streets, though he would suffer from a severe case of the Bleeding Effect for most of his life. Later on, he was discovered by a female Assassin by the name of Hannah Mueller, and after a series of events that led to him rising through the ranks of the Assassin Order, Daniel's subconsciousness forced him to kill the modern day Mentor on 6 November 2000.
He later returned to an Abstergo facility in Philadelphia, where he was again placed in the Animus under the supervision of Warren Vidic, and his own memories were viewed to obtain the locations of all of the Assassin camps he had visited, along with those of his ancestor, Nikolai Orelov. Following this, Daniel later ended his Animus sessions and joined the ranks of the Templar Order.
Subject 12 was forced to relive the memories of an ancestor related to the Philadelphia Project, in which the USS Eldridge briefly manifested in a future state for approximately 18 minutes, due to the usage of a Piece of Eden. Using recovered data, Abstergo was able to reconstruct the original artifact used in the experiment.
Subject 14 was a man who experienced extreme problems as a result of the Bleeding Effect. 
During 2010, the Animus Project was focusing on Subject 15, a pregnant woman who eventually started suffering from the Bleeding Effect. She experienced "memory-within-memory" patterns due to the memories of the fetus' father conflicting with her ancestors' memories.
Eventually, in mid December 2010, Lucy Stillman noticed that Subject 15's Raphe neurons were activating at an accelerated rate, and that the Animus was somehow inducing an incomplete state of dream-sleep. When Lucy informed Vidic of Subject 15's dangerous state, Vidic concluded that they had already gathered enough material from her, and subsequently contacted Steve Gibbs to send a disposal unit to remove Subject 15.
In 2011, Abstergo kidnapped Clay Kaczmarek, a member of the Assassin Order who specialized in computer hacking and engineering. Dubbed Subject 16, Clay was placed into the Animus at Abstergo's Rome facility for several months, in order to obtain the location of one of the Apples of Eden, with some of the Animus sessions lasting for days at a time.
As Clay was psychologically unable to maintain these sessions for such extended periods of time, the personalities of his ancestors began overlapping with his own.
Eventually, Vidic discovered that Clay was a direct descendant of Adam, one of the first Human-Isu hybrids and an individual amongst the first few to rise up against the pre-existing species. Through reliving Adam's memories, Clay and Vidic obtained the secrets of the Assassins and the First Civilization, though realizing his mind would soon disappear entirely, Clay hacked the Animus some time after and placed an AI construct of his own personality inside the Animus, that only the next Animus Subject would be able to activate.
Clay also left behind several hidden Glyphs and Rifts throughout the memories of another of his ancestors, Ezio Auditore da Firenze. Following this, as he delved into insanity as a result of the Bleeding Effect, Clay wrote various cryptic messages with his blood across the Animus room and his own cell before eventually committing suicide using a ball-point pen, with Lucy bearing witness.
In September 2012, Abstergo captured their next Subject, number 17, a bartender by the name of Desmond Miles. Prior to his capture, Desmond ran away from his Assassin parents at the age of 16, and was discovered to have a high concentration of First Civilization DNA in his genes.
At first, Desmond was directly put in the Animus and forced to relive the memories of Altaïr Ibn-La'Ahad, a Levantine Assassin, and upon reaching Abstergo's target memory, a map displaying the locations of several Precursor Temples around the world erupted from an Apple of Eden, prompting the company to have no further use for Desmond. While Vidic's superiors ordered Desmond's disposal, Lucy Stillman managed to convince them of Desmond's use to Abstergo, maintaining his life.
Not too long afterwards, Lucy, who was previously an Assassin and a secret Templar, escaped the Abstergo facility with Desmond and relocated to an Assassin hideout, where Desmond relived the memories of Ezio Auditore da Firenze in a recreated Animus, unknowingly helped in part by Lucy and Vidic's secret plan.
After Desmond's escape, Vidic then turned his attention to the Animi Training Program, which held the objective of training Abstergo agents using numerous Animi and making them relive the memories of Templars, Assassins and unaffiliated individuals of interest through extracted memories, so that the agents would be able to combat the remnants of the Assassin Order with their newly accumulated skills. The project eventually resulted in the promotion of Juhani Otso Berg to the rank of Master Templar, who was immediately assigned to capture the Assassin leader William Miles.
Abstergo also started Project Legacy after Desmond's escape, which made subjects sift through the extracted memories of important individuals, with the aim of finding out more about the Assassin Order and the Pieces of Eden. The project was put on hold after repeated security breaches caused by Erudito.
On 14 December 2012, Vidic was killed by Desmond Miles at Abstergo's Rome facility using an Apple of Eden. Even though Abstergo lost the world's leading expert in genetic memory and the pioneer of the Animus, the next phase of the Animus Project would proceed as planned with David Kilkerman as Director.
A week after Vidic's death, Desmond Miles' body was discovered in the Grand Temple. The Sample Recovery Unit #3 led by Case Fisher extracted several DNA samples and vital organs from Desmond's body, preserving his legacy as the "Sample 17", which was uploaded to the Abstergo Cloud.
Using the Abstergo Entertainment's employees as researchers under the guise of creating entertainment products, Abstergo explored the memories of several of Desmond's ancestors with the hope of obtaining any useful information related to the Sages or Precursor technology.
- In the non-canonical modern day storyline of the Assassin's Creed French comic, an Assassin named Jonathan Hawk was placed in a futuristic Animus to relive the memories of his ancestors Accipiter and Numa Al'Khamsin.
- ↑ 1.0 1.1 1.2 1.3 1.4 Assassin's Creed: Brotherhood
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Assassin's Creed
- ↑ 3.0 3.1 3.2 Abstergo Industries' website
- ↑ 4.0 4.1 Assassin's Creed: The Fall - Issue #1
- ↑ 5.0 5.1 Assassin's Creed IV: Black Flag
- ↑ 6.0 6.1 6.2 6.3 6.4 Assassin's Creed Encyclopedia
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Assassin's Creed: The Fall - Issue #3
- ↑ Assassin's Creed: The Fall - Issue #2
- ↑ Assassin's Creed: The Fall - Epilogue
- ↑ Assassin's Creed: Heresy
- ↑ 11.0 11.1 11.2 11.3 Assassin's Creed II
- ↑ 12.0 12.1 12.2 Assassin's Creed: Revelations
- ↑ Assassin's Creed: Revelations - The Lost Archive
- ↑ 14.0 14.1 Assassin's Creed: Initiates
- ↑ Assassin's Creed: Project Legacy
- ↑ Assassin's Creed III
- ↑ Assassin's Creed: The Essential Guide
- ↑ Assassin's Creed 3: Accipiter