A hapless, hopeless and unremarkable young man one day finds himself to be an impediment his very reality when a pair of unusual men come up to him and apologize for his sudden lack of existence in the world he's come to know all his life. His home. His family. His friends. None of them knew who he should have been to them anymore and his very identity was now apparently entirely foreign to this world.
The apologetic pair whisk him away to a strange room that couldn't have fit inside the toilet he was once familiar with but before he could make sense of the strange instruments he sees before him, the men explain to him that his world is one of many simulations made to reenact events in their history as a way to figure out the truths behind them. These simulations aren't perfect though, and they need the occasional adjustments to course correct their simulations to bring things in line with the reality they have on record. The man's mishap was a result of this occasion's adjustment.
Unfortunately for our protagonist, his continued presence in their simulation managed to somehow prevent the emergent prophet of his age from writing up his doctrine at every turn. They've tried to remove him before within the bounds of his reality but even that led to complications down the line so their only option was to extract him completely. The curious thing however is that while history does seem set back on track, he actually was known to have existed in true reality and played a part in the formation of the new world order yet his existence in the simulation was paradoxically throwing everything off. That's why they took him out of it and why they need his help to understand what's really going on here.
Another plot that seems right up Will Ferrel's alley. I definitely wasn't thinking of him at the time this was written up but for reason he just fits into this role. I must confess I pulled a JJ Abrams on the reason for the paradox and didn't think so far ahead for it but the feel of the story would have been a character drama where the MC gets to see his world without him and the prophet character would have been unable to go on to greatness without a few pushes the MC gives down the line in the story. The twist would be that the Bible 2.0 the prophet comes up with was never divine in nature and was a self-help book he came up with to get himself through life that later had divinity attributed to it when some ardent fans got super zealous on its effectiveness. I didn't come up with that to make a snide implication at the origins of christianity writing that sentence but frankly my thoughts on the matter does in fact line up with it. Funny that.