For those who have finished all the Ancient Mechanisms in Origins, i'm sure you walked away with the feeling that the Isu are telling us we might be in a sim. It seems others have also walked away feeling the same way. The world of AC is not what it seems.

This theory also supports why the bleeding affect happens and how the current character Layla's experience with non-relatives and how the Isu can see the future. The Isu really do not see the future, but accepted they are in a sim and worked inside those limits. Knowing the code, you can see what future events the code will send your way.

REDDIT - Assassin's Creed Simulation Theory: Ancient Mechanism Spoilers

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The Isu ran simulations until they themselves discovered they were in a simulation, and then promptly discovered the source code behind the simulation. Throughout the dialogues, they basically say that after this discovery, while they could alter things on a small scale, they also discovered that there was little they could do to actually influence the natural progression of the simulation. In their own words, they could only ever truly "observe, not truly interfere/change/alter". Their society fell into a society of control and order, because this gave them some solace when faced with the truth.

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Remember that weird little experiment explained by Juno in the grand temple? She explained that an Isu could literally take a group of humans, command them to think of a tree before them with the apple, and then (for some reason) a literal fricking tree would just magically appear. (Didn't that seem weird to anyone else?) The hope of this experiment was to launch enough pieces of Eden into orbit, and then have everybody on the planet implore (something? coughThe source code?cough) to "save us". The plan was to literally gather enough human/Isu minds to influence some unknown force around the entire planet, and prevent a disaster like a node hard-reset from resetting them as well.

This plan only failed due to the fact that they were unable to direct the peices of eden in a way that allowed them to successfully accomplish this task. This same issue (and desmond), thwarted the Templars from attempting the same thing to control the world with their own satellite (though they are of course unaware of the true reality of their simulation, and only meant to use it to control human populations).

The machine that Desmond activates right before his death is actually a device similar to the attempted experiment Juno previously mentioned. Both Minerva and Juno seem to indicate inside of the grand temple that the universe has some sort of underlying source code, and that it could be slightly altered to stop the catastrophe.