The Templar Order, aka Abstergo Industries, invented the first version of the Animus in the 1930s with knowledge gained from an Apple of Eden. Their goal was to be able to look through the eyes of their ancestors to locate Pieces of Eden; however, they probably never thought of the future implications of the Animus. For instance, what would happen if someone's ancestor used an Animus while being simulated by their descendant in another Animus?
The Animus is essentially a VR device that simulates what the 's ancestor lived through. s cannot make their own decisions or change the past. Attempting to do so through actions like killing civilians leads to desynchronization and forces the Animus to reset. In order to use an Animus inside an Animus, the 's ancestor (or simulation of someone else's ancestor) would need to have used one at some point in their life.
While this has yet to occur in game, Assassin's Creed: Revelations gives a glimpse at what it might look like. In trying to learn about the foundation of the Assassin Brotherhood, protagonist Ezio stumbles across Isu Memory Seals left behind by his ancestor, Altaïr. These show Ezio Altaïr's past, meaning present-day protagonist Desmond relives Ezio's memories of watching Altaïr's memories. Still, Ezio isn't embodying Altaïr - he's merely watching his memories. The question remains: How would using an Animus within an Animus play out?
Assassin's Creed Animus-ception: It's All A Simulation
After Desmond's death in Asassin's Creed 3, Abstergo recovers his body and assassin DNA, but it needs a way to explore his ancestors' lives in a quick and efficient way. In AC4: Black Flag, Abstergo gives the Animus a major redesign, creating a new branch of the company called Abstergo Entertainment and turning the Animus software into a VR game engine called the Animus Omega. This becomes the modern-day vessel for players to relive the life of AC4's Edward Kenway, and it also shows nothing special would happen in the Animus-Inception scenario because, in a way, it's already happening in real life.
Ubisoft began making Assassin's Creed more "meta" around this time. Black Flag shifted the present-day segments from following a distinct character in third person to a silent one in first parson. Like real-life players of AC4, this protagonist views their own life in first person and Edward's life through a video game. More recently, Ubisoft went as far as to make the logo for the series' real-life game engine, Ubisoft Anvil, the same as that of Abstergo Entertainment. If the meta-narrative is positing that the Animus Omega is the same thing as Ubisoft Anvil, players have essentially been using the Animus engine to play as a character who's using an Animus to relive the life of an assassin.
In all likelihood, if an AC game showed someone in an Animus using an Animus, they would just see what their ancestor sees: another ancestor. The Assassin's Creed comics do take this idea a step further, questioning whether there is even a present reality or if it's all just a simulation. Either way, the would just go through the journey the same way real-life players do. It may not be the most exciting answer, but it's interesting to see how many unique ideas and questions Ubisoft has created by making Assassin's Creed such a meta experience for "players" both real and in game.