The resignation of National Security Adviser Michael Flynn on Monday evening raises troubling questions about the role of the Federal Bureau of Investigation (FBI) and the intelligence services.

Flynn ostensibly resigned because he provided Vice President Mike Pence with “incomplete information” about a conversation he had with the Russian ambassador, which turned out to include a discussion of recent sanctions, contrary to his earlier denials. Trust is crucial; the resignation was warranted.

That said, the sanctions were largely bogus, and were applied not just to punish Russia for spying on the U.S. (both countries clearly spy on each other), but to substantiate the Democratic Party’s sore-loser conspiracy theory that Russia was responsible for electing Donald Trump.

There is no concrete evidence to support that theory, and there is no evidence (yet) that Flynn did anything but discuss sanctions in the most general terms. He did not break the Logan Act, nor any other law, apparently.

Whether Flynn deliberately concealed the contents of his conversation from Vice President Pence, or merely forgot what had been said, he was “caught” because the Department of Justice had been eavesdropping on the conversation. And one of the officials responsible for ordering the eavesdropping was none other than Acting Attorney General Sally Yates, who forced President Trump to fire her when she defied her duty to enforce his executive order on immigration, however, controversial.

Four possibilities emerge. One, which the media and the Democrats (largely one and the same) clearly believe, is that Flynn really was a potential Russian plant, perhaps indicating much deeper Russian penetration of the campaign and administration.

A second possibility is that things really are what they seem, on the surface, to be. Russia’s unusual response to the sanctions — declining to retaliate — was so bizarre that it warranted investigation, which then raised legitimate suspicions about Flynn.

The remaining possibilities are more worrying. The third explanation is that President Obama deliberately, and cleverly, used the bogus sanctions as a “blue dye” test to expose which strings Russia might try to pull to relieve them. Flynn, with a prior relationship with the Russian government, may have been a natural, innocuous point of contact — or perhaps something more.

The fourth and most worrying explanation is that the government was not merely monitoring the communications of Russian diplomats, but of the Trump transition team itself. The fact that the contents of Flynn’s phone conversation — highly sensitive intelligence — were leaked to the media suggests that someone with access to that information also has a political axe to grind.

Democrats are clamoring for a deeper investigation of Russian ties to Trump. But the more serious question is whether our nation’s intelligence services were involved in what amounts to political espionage against the newly-elected government.

We know that there are hundreds and perhaps thousands of federal bureaucrats already using shadow communications systems. How far does that “shadow government” go?

The FBI, CIA and other agencies ought to reassure Congress, or come clean.

Joel B. Pollak is Senior Editor-at-Large at Breitbart News. He was named one of the “most influential” people in news media in 2016. His new book, How Trump Won: The Inside Story of a Revolution, is available from Regnery. Follow him on Twitter at @joelpollak.