The trouble is that it gets used sometimes to imply that the official version is more than just a theory, which often is not the case.

The official version about Saddam's Weapons of Mass Destruction was very much a Conspiracy Theory, and one which was a lot further from the truth than theories of the time that disputed it. I think that's also quite conceivably the case in a number of current matters.

Under Trump I am afraid we can anticipate that a lot of official versions are going to be false, and that the actual truth is going to be denigrated as a conspiracy theory.

Pretty well always there is one conspiracy theory that actually is true.
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I wouldn't really regard the sedevacantists as comprising a conspiracy theory. I'd see them as a conspiracy. It's not so much that their ideas are daft, but that they are just wrong. Of course the people who hold them tend to be daft, but that's another matter. I get the impression they are more visible in the USA than they are here.