The basic theory behind the Animus is that all animals, including humans, have genetic memories from their ancestors which allow them to intuitively know what to do in certain situations. However, going far beyond basic instincts, genetic memories actually contain a permanent record of all of the memories ever experienced by each and every ancestor of a given individual. The Animus is a machine which can render the user's genetic memories, or those of their ancestors, as a full 3-D simulated world, which can be viewed and recorded by the outside operators. The user however, cannot simply access any memory with zero preparation; without confidence and some Synchronization with the ancestor's mindset/personality/etc. the memory is clouded and causes the user mental discomfort to view. This required Synchronization, can be learned/acquired through accessing "easier" memories. The Animus is capable of experiencing the memories of everything that happens to an ancestor, even moments they themselves would not have been able to remember, such as their birth, continuing forward until the moment when they take part in the conception of the next ancestor in the user's family tree. At that point, their genetic information is passed on, so no further direct reading is possible.
Throughout the series so far, Desmond Miles, the main character, uses the Animus to see the memories of his ancestor, the deadly assassin Altaïr , active during the time of the crusades. He sees the simulation as it plays out but is also supposedly controlling Altair as if the avatar of the ancient Assassin was his own body. if the player "dies" in gameplay, history is not altered, it is merely Desmond's experience becoming "de-synchronized" with what actually happened to Altaïr. Also, while using the Animus to view the genetic memory of long dead ancestors, something even weirder occasionally happens during the recorded memory. A memory glitch will occur, which allows the viewer to experience that portion of the memory from some sort of enhanced perspective. It is believed that through the over-use of the Animus it causes a 'bleeding effect where the subject is unable to distinguish between reality and the experiences inside the Animus. This is hinted at the end of the first game whereby Desmond is able to use Eagle Vision to see messages and symbols written in blood, presumably by a previous Animus user.
In Assassin's Creed II, Desmond begins to use the Animus 2.0, this time to re-live the memories of a different ancestor named Ezio Auditore da Firenze. It is revealed that the Animus 2.0 allows its user to learn the skills of their ancestors through re-living their memories. This bestows Desmond with the skills learned by Ezio, as well as certain side effects gained from overuse of the Animus.
The multiplayer component of Assassin's Creed: Brotherhood takes place inside an Abstergo facility where the players (as Abstergo agents) each use their own Animus to recall abilities that earlier Templars had through the bleeding effect and use the simulations to train for real-world combat. The only notable change here is that the agents are experiencing the memories of an individual they are not related to. This continues in Assassin's Creed: Revelations where the player is told more specifically that their success in the Animus training will grant them deeper access to Abstergo's inner circles and the company's secrets.
Created by the Assassins, the Animus 2.0 is an upgraded version of its predecessor and was introduced in Assassin's Creed 2. The operator and designer of the machine, Rebecca Crane, claims the Animus 2.0 is faster and "twice as awesome" as the one created by Abstergo Industries. In addition to a new look, upgrades include a more streamlined user interface which contains a database capable of storing historical information on important landmarks, characters and documents as the user encounters them in their memories.
The Animus 3.0 was constructed while Desmond was rendered comatose after the events of Assassin's Creed: Brotherhood. Being mainly a software upgrade, the Animus 3.0 featured a new user interface and slight changes to how the user controls their ancestor within a memory. On the hardware side, the Animus 3.0 was made significantly more portable by being only a head and armrest, needing only a flat surface for the user to lie on.
The word Animus is Latin for courage, spirit, soul, intellect, memory, and consciousness.