Jupiter Ascending happens, which leads to humanity being introduced to galactic civilization. The resulting technological boom leads to the world of Speed Racer but then later it leads to the creation of the AI that build the Matrix. Each of Cloud Atlas’s eras is the same handful of test subjects being plugged into prototype versions of the Matrix. The events of the movie Bound are what the machines identified as the pinnacle of human civilization, which is why the version of the Matrix resembles the late 1990s. Sense8 takes place within the Matrix, which is the mechanism by which these human minds connect to each other (and it’s more specifically the version that NPH ran because it no longer resembles the late 1990s).

The AniMatrix is not part of the canon because they didn’t direct it.