Now this is all tongue in cheek and may only serve as a basis for a fictional short story at best. But it plays out like thus...

Posit: Let the rapture to have actually occurred. Let God to have judged the mass of humanity and to have found it wanting and lacking.

But a small statistical number of persons were taken. These persons would be counted toward local city or municipality "missing persons".

Investigators through the course of uh... investigating, come across similarities among these missing people. Then events are triggered.

Where investigators are linked or brought in contact globally and the disappearance is attributed to roughly 6pm. Local time.

And then the horror of what happened unfolds and events start occurring in the world and the investigators feel the need to take steps to...

...do some protagonistic steps since they are the only ones "clued in". To attempt to save or [insert trite moral platitude here] humanity.

While the judgement clock ticks down. It's a race against time. Forced to conform within their day jobs and unable to reveal the truth...

Or attempts to reveal the truth are laughed at or "celestially" altered. Or perhaps they happen to meet an Angel doing Gods work...

...to do some catastrophe or what-have-you. Or just have one there for awesome dialogue and plot device. Etc.

Write it!

I like the notion that technically it came and went. And statistically speaking the number who were found worthy was so numerically...

...insignificant that they were just attributed to innocuous cases of missing persons. Until people put clues together.

It makes for a good premise.