There is a hierarchy of reality in AC. Despite Desmond being as bland as a... Well, as a protagonist from an odd-numbered Assassin’s Creed game, the Desmond-reality helps me when I’m struggling with the bizarre behaviors exhibited by the historical-reality, like repetitive shouts from the guards, or leaping forty stories to land safely into a pile of hay.
On the very first level of the hierarchy of reality is the reality of the player. That’s you! The ones sitting on the couch, controller in hand, managing saves and loads and pressing left control and A and whatnot.
One level below the player is Desmond’s reality. This is the future-plot, where Desmond is kidnapped and shoved into the Animus. Desmond, as directed by the player, picks up skills from his ancestors as he explores their memories, and occasionally the game cuts Desmond loose to demonstrate his capabilities at free-running, etc.
Desmond-reality is also the layer in which the Animus codex entries and logic are written. In Desmond-reality the Animus has its own set of rules—you can’t go here, guards are a bag of simple and repetitive behaviors and shouts, courtesans take money and grant camouflage, and so on. The Animus is a simulation meant to help Desmond explore memories, and the simulation created by the Animus has rules to enforce memories are “properly synchronized”.
One level further down, contained wholly within the Animus, are the ancestral memories Desmond experiences. This is not exactly the same as player-reality’s history, but a plausible (well... plausible-ish) alternate history confined within the entire Assassin’s Creed game. Just as Desmond isn’t aware of the player-reality, memory-reality is not aware of Desmond-reality. Guards are all instantly aware of all your crimes, and get slaughtered by the boatload only to respawn minutes later, but do not see anything unusual with these circumstances. They aren’t aware of the counterattack marker or detection meters above their heads.
As it turns out, the rules dictated by the Animus simulation in Desmond-reality happen to match up with Desmond’s perception of a video game. By happy coincidence, the Animus rules also line up with the player-reality expectations of a video game as well! In Desmond-reality, the Animus says you have to follow memories in chronological order, much to the dismay of Desmond’s captors.
In player-reality, this is lampshading our expectations of narrative video game structure, where we expect a linear structure of events to take place in a game-world populated by non-player characters whose behavior is repetitive and predictable. As players we expect some method of evading guards, and the fiction of Desmond-reality draws from the fiction of memory-reality in order to create courtesans whose function is to camouflage your presence. The presence of the Animus and Desmond-reality is a convenient bridge between the player-reality, where we understand video games contain objectives and the tools to fulfill those objectives, and the historical-reality, which has very little to say about detection meters, or collectible flags scattered across ancient cities.
My favorite parts of AC all lay on the boundaries between these realities . There’s a particularly clever moment in AC2 where Desmond is informed his time in historical-reality has the potential to affect his perception of the world around him. In player-reality, we’re probably aware of this in the form of dreaming about Tetris, or walking outside and thinking the real world has really great draw-distance. Sure enough, at one point Desmond sees historical-reality guards charging at him from the walls. This creepy moment is compounded by the player’s reaction, where the sudden appearance of enemies has us instinctually frantically mashing the attack button out of shock. In this moment, all three realities converge on a single moment of flailing terror. 
There are many, lesser convergences in Assassin’s Creed. Part of the fun is being able to examine player-reality history as presented by memory-reality: comparing what we know of history (The Borgia! The Colosseum! The Crusades!) against the ability to explore these things in a simulation, or being able to watch the things in our player-reality contrast against the memory-reality, as when Ezio saves the world from Leonardo da Vinci’s invented tanks and submarines.
Of course, these meetings of reality can also cause problems. I was very irritated that the treatment of Native Americans at the hands of the colonials went virtually unmentioned until 2/3rds of the way through the game, where you are finally confronted with the truth. Conor, in the memory-reality, acts horrified, yet this revelation hardly changes his relationship with Washington. Meanwhile, in player-reality, I was already very aware of the horrors surrounding the founding of the United States. The “secret” revealed by the game was actually something I had spent the entire game anticipating. The competing realities, in this case, severely diminished the impact of the twist.
Other rifts between my player-reality and the memory-reality exist. There’s the ride of Paul Revere, the fact that the Boston Tea Party was turned from covert vandalism into an outright bloodbath, and Conor’s bizarre presence at the signing of the Declaration of Independance. In all these examples, the rift between what I know in player-reality and what is presented as memory-reality is just too great for me to handle, and its done in such a way that the Desmond-reality can’t (or doesn’t) act to smooth the bumps over. Secret aliens and grand conspiracies are one thing, because they are acknowledged within the Desmond-reality. To have the bridge of Desmond-reality and not use it makes the situation so much worse.
: Please check out Robert Yang’s post on virtual/real architecture for a really cool discussion on realty/unreality and how players bridge that gap. I think it also explores why the Animus is such a powerful tool as it helps us reconcile our multiple realities.
 Digital dualism: “our reality is both technological and organic, both digital and physical, all at once.” When I reacted synchronously with our Desmond avatar, I formed a bond that was like a little bit of the Desmond-memory synchronicity the game harps on so often. I, like Desmond living in memory-reality, was having a physical reaction to a digital phenomenon.