The Big Bad Shuffle

Some works have a clear, outstanding Big Bad. Others like to play it tricky with The Man Behind the Man. And then there's this. Not even The Chessmaster really seems to know who's in control, and on the off chance that he does, nobody else ever will. When Jack defeats Mr. Corrupton, learns that Corrupton was really just being misled by Dr. Unethik, kills Unethik, finds out that Unethik was secretly controlled by a shadowy government conspiracy and investigates them for a while before learning that one of the people on their Omniscient Council of Vagueness was Mr. Corruption (who nevertheless may be doing it all at the behest of his scheming trophy wife), the writers are playing the Big Bad Shuffle.

This will often involve a Gambit Pileup, as in the above example. But, where the Pileup deals with all these manipulators thwarting each other, this Trope is about the plot's cascading secrecy as to who is really in control. Multiple Reveals and UnReveals are almost mandatory. Contrast Big Bad Ensemble, which is when there are several Big Bads operating at once, regardless of how they may or may not impact on one anothers agendas.

Literature

 * A Song of Ice and Fire: Good luck guessing who is ultimately behind any given act of villainy.
 * So, in the Molly Moon series, there's Primo Cell, who's really being controlled by  But then we learn that the real person with the strings is   Okay... And then in the third book, it turns out   hypnotised   into   Start of Darkness. Wow.

Live Action TV

 * Angel: Darla wants revenge/reunion with Angel. Her actions prompt Sajhan to pull Holtz through time to kill Angel and Darla both. Holtz betrays Sajhan, who then seeks aid from longtime foes Wolfram & Hart, who play off both Sajhan and Holtz. Sajhan discovers this and banishes Holtz to another reality, then duels Angel. In the aftermath of that battle, Holtz returns with a new means of attacking Angel, while Wolfram & Hart lick their wounds. Who was the Big Bad? Not even Joss Whedon could tell you.
 * The writers, same as every season.
 * A later Big Bad takes credit for having set all of it in motion millennia ago as part of their plan to (re)enter and take over the mortal plain. The veracity of the claim is never tested but there's no evidence to dispute it either and several of the events involved would definitely make more sense with some otherworldly party pulling strings behind the scenes.
 * Burn Notice season three started with a Big Good cop as the potential antagonist, then moved on to an Affably Evil fixer, followed by a Psycho for Hire, and culminating with a Terrorist Without a Cause. Apparently feeling that was too easy, the writers in season four go with The Mole, a Corrupt Corporate Executive, a stray Smug Snake, a returning Evil Counterpart, ANOTHER returning Evil Counterpart, all before the reveal of the actual Big Bad:

Video Games

 * The Metal Gear games, especially the Mind Screw of Metal Gear Solid 2, and the non-canonical Ghost Babel, where the terrorist general, his mercenary Dragon/manipulator, and the U.S. government all mock the others as fools who are just being played by whoever is mocking at the moment.
 * Untangling who stands behind whom, with many false leads, is the entire point of Deus Ex.
 * Super Smash Bros Brawl, in the Subspace campaign, has... numerous Big Bads. This stems partly from the nature of the game - as a lumping together of the respective Nintendo mythologies, all the key villains come with their respective heroes.
 * Myst has this in spades. The game begins when you meet two imprisoned brothers, each of whom tries to convince you that his brother is the one behind the disappearance of their father. As you complete the various stages to slowly free the brothers, you encounter clues to help you finally decide which of the two is the actual Big Bad.
 * Seiken Densetsu 3 has three possible Big Bads, each with their own dragons and Mooks. About halfway the game, one of them will eliminate the other two (which one depends on your choice of main character), but until that time the whole game is a tangle of their conflicting plots.
 * Batman: Arkham City has Hugo Strange and The Joker competing for the position of Big Bad,
 * You could argue that Persona 4 is filled with this. First it seems that is the killer but  The murder attempts continue and you eventually find out that the one doing the deeds was  but then it turns out  The person who made him snap was  who  AND THEN  AND FINALLY  And I'm out of breath...

Western Animation

 * One episode of Gargoyles featured six villains, each revealing one after the other that the previous villain wasn't actually that episode's Big Bad.