The how is likely just another question of physics; I recall watching some PBS special that hypothesized some collision of higher-dimensional branes.
Even in this universe, it's possible to be entirely cut off from regions. What does a black hole look like inside its event horizon? We have models, but it's impossible to measure. On a larger scale, assuming the continue expansion of the universe, the furthest galaxies will eventually be receding from us faster than the speed of light, making them un-observable.
The fundamental question is: what's the most basic truths that we can ever know?
If there are hyperdimensional branes the likelihood is that we wont be able to learn much about their origins because of their relationship to our universe. An acceptable answer then becomes "We can't know how they exist..."
Brane theory was what came to mind immediately for me.