We Have Been Researching Phlebotinum for Years

"Mulder: They're here, aren't they?

Deep Throat: Mr. Mulder, "they" have been here for a long, long time."

- The X-Files

The Hero encounters some weird shit. Really weird shit. However, just as he is about to say bye-bye to his sanity, some impeccably dressed gentlemen take him into a sciencey lab where The Professor explains that what the hero saw was a perfectly scientific phenomenon they've studied for years, and really, just another kind of Applied Phlebotinum that The World Is Not Ready for yet...

This trope is a form of Exposition that would have become an Info Dump, if it wasn't so long overdue, since it comes after the protagonist (and the audience) is thrust right into the middle of a situation he cannot even begin to understand. It doesn't have to be Phlebotinum per se: any kind of Masquerade will do, as long as the hero stumbles into a life-threatening situation before people who know what's going on show up. The inverse of this is Theory Before Phenomenon.

Anime and Manga

 * In the first two episodes of Darker Than Black The Hero accidentally saves a scientist working under the Masquerade and on the run receives a hasty explanation of what's going on. Of course, the true nature of the series is shown only.
 * Neon Genesis Evangelion begins with this very trope. Shinji, a slightly disfunctional boy, witnesses an Eldritch Abomination attacking the city then is promptly thrown into the cockpit of a Humongous Mecha that's not really a mecha at all: it's alive and is VERY bloodthirsty. It takes a few episodes until he gets the explanation about what the hell is going on but never gets told about what he's piloting until three episodes from the end. It's unclear which is worse: that he was told so late or that he was told at all. Regardless which one is true, Shinji got an all-expenses-paid visit to the Despair Event Horizon for his effort.

Film
"Dr. Scott: This sonic transducer...it is, I suppose, some kind of audio-vibratory-physio-molecular transport device? Brad: You mean...?! Dr. Scott: Yes, Brad, it's something we ourselves have been working on for quite some time. But it seems our friend here has found a means of perfecting it. A device which is capable of breaking down solid matter and projecting it through space...and who knows, perhaps even time itself!"
 * Independence Day, when they visit Area 51, it turns out The Government knew about the aliens all along.
 * In the first Underworld movie, when Selene tells Michael about the werewolves and the vampires.
 * Rocky Horror Picture Show:

Live Action TV

 * The spaceship containing the Power Source of the chronosphere from Seven Days.
 * Happens all over the Myth Arc of The X-Files.

Video Games

 * Max Payne: "We were all involved in the early stages of the Project during the Gulf War..." This refers to.
 * In Half Life, it's revealed in Opposing Force that

Webcomics

 * Weregeek begins with Mark drooling at a look on dice and being chased by The Hunters. He is saved by Joel and the others, who explain to him that he is a weregeek, just like themselves, which is why he was being hunted. It is much later explained that.