Let me build on top of 
The universe is a computer simulation
Also read this post's Part 2 and Part 3. Part 4 coming soon.
Take that for granted through this post. Just assume this is the absolute truth. It's our starting point. Okay, carry on. Think of The Sims, a game in which we influence a family to develop according to our will while catering to their needs. Or something more recent, like Virtual Reality chat apps to dive in and just hang out.
Most of our games put humans as the protagonists or keystones of the enviroment. From first person shooters and rpgs to sandboxes and simulators, almost everything has humans in it. Likewise, the creator of our simulated universe is human. We are NPCs to them like the villagers walking around in any MMORPG are NPCs to us.
Our grand design
Combine an extremely technologically advanced form of the two ideas and you get a playable universe simulator. Something you can login to play god by enabling cheats or just features player characters that can walk on water or turn water into wine.
Our creator would have named himself Jesus Christ, fooled around a bit on our planet, then logged off, leaving the computer on without closing our executable. Maybe there's no pause feature. Either that or we're an idle game, so when Jesus'es computer is turned on again, time flow is calculated retroactively.
Unless we're not entertainment. "What if that thing happened instead during this event of our history?" This question started our project, which functions as a hypothetical but historical scenario simulator, much like Europa Universalis.
Extra puzzle pieces
The paranormal and supernatural are then explained by someone clicking near us (or whatever they use) and invoking some kind of interaction we don't quite understand. Again, Maxis players will easily understand this. Who hasn't loaded up Sim City only to randomly summon multiple tornadoes on a chaotic win!
Just remember: even if we are all NPC's, there's always that one random encounter that hits the player so hard, he gets the game over screen. Let us be this.
[image source: Maxis' The Sims, Maxis' Sim City 3000 screenshot by Looneyboo]
Thank you for reading!
There is a Part II and Part III now available if you have a bit more time.