Idea courtesy of apostate, who found the 'What if...?' text in his Facebook feed. If you're coming in late, you can start at Part I.
Part IV: Scientific Analysis
"Gentlemen, I'd like to hear your reports. Dr. Myers will go first."
"Thank you, Mr. President. You know the broad outlines, of course: two days ago, a selection of holy books started behaving like two-way radios, offering direct communication with Heaven - or so the people contacted consistently claim. These conversations appear to have a physical component: that is, the words spoken are ordinary sounds. In some cases the text appears to rearrange itself to match the words being spoken. These effects can be recorded using standard audio-visual equipment. In addition, there appears to be what, for lack of a better explanation, I'm going to call a mental effect: anyone who participates in these conversations comes away absolutely convinced that they've been speaking to Jesus, the Voice of God, or one of the angels. You can suggest alternative explanations, and our test subjects seem to be able to consider them, but none of the test subjects has any doubt about what actually happened. No matter how plausible the alternative explanation, nobody who has had one of these conversations can be convinced to doubt that they were actually speaking with Jesus, or one of His appointed representatives."
"Mr. President, I hope I don't have to explain to you how dangerous this is. We're talking about mind control on a scale that staggers the imagination. As far as we can determine, it's 100% effective - but so far, we haven't been able to determine even a hint of a mechanism for it. In other words, we don't know how it works. We don't know how it might work. We don't even have any good guesses. And, as a result, we have no idea what other sorts of beliefs or commands may be implanted at the same time."
"Do you have any idea where it might be coming from?"
"Well... All of our test subjects insist that they've spoken to Jesus; that is, to an aspect of an eternal creator who is all-knowing and all-powerful and exists outside of space and time. Galling as I find the idea personally, from a scientific perspective it would be a mistake to dismiss the possibility that that's really all there is to it. Such a being could do anything it wanted to, including this. If that's the case, then it doesn't really answer any of the obvious follow-up questions: Why would such a being choose to do this? Why now? Why this way?
"...Mr. President, I know you were raised as a Christian. I assume you were taught that not only does such a being exist, but He takes a direct interest in His Creation, and has a personal relationship with His worshipers. I want you to set that aside, and consider for a moment what it means to have a personal relationship with something so completely alien. What would humanity even look like to something that exists outside of time? What do our choices mean to a being for whom, in a sense, everything is always happening at once? How do you understand an entity like that?"
"That's a rather disturbing perspective, Dr. Myers."
"If it makes you feel any better, Mr. President, it disturbs me, too. The next possibility is that we aren't dealing with anything divine, but rather with a technology so advanced that we can't tell the difference. I'm sure you've heard that any sufficiently advanced technology..."
"...is indistinguishable from magic. Yes. Please continue."
"Well, if we are dealing with aliens, their cloaking technology is as advanced as their communications. SETI, NASA, and about a billion amateur astronomers around the globe have found exactly no evidence of anything out of the ordinary. Of course, many of the people involved have already opened their Bibles, so there's always the possibility that they've been commanded to overlook an alien presence, and aren't even aware of the command. We're doing what we can to check that, but we're running out of people who haven't been exposed yet. And it seems equally likely that if there is an alien presence, our equipment simply isn't capable of detecting it."
"So whatever this, we're completely at its mercy."
"Yes, Mr. President. That's pretty much it. If this is being done by aliens, and if we can isolate a mechanism for it, and if we can locate them, then maybe we can do something... though if they're that far ahead of us, it's hard to imagine what; I'm pretty sure we won't be able to hack into their mothership's mainframe using a stolen space-fighter and a Macbook."
"Very well, then. Is there anything else, Dr. Myers?"
"One thing more, Mr. President. The... mental effect... appears to be restricted to direct contact. That is, you can listen to a recording of someone talking to their Bible without necessarily being persuaded that you're hearing the voice of Jesus. Some of my colleagues have experimented with asking questions through an intermediary - that is, trying to get answers without exposing themselves directly - but they haven't received much in the way of explanations. The Jesus-voice simply insists that it is, well, Jesus, and that the people He speaks to become convinced because this is true. As scientific answers go, that isn't much help. But you might be able to use that method to get answers on other subjects without being exposed yourself."
"How much more blessed are those who have not seen, and yet believe... Yes, I see. That does seem the safest course. Thank you, Dr. Myers."