The X Files is back, and the conspiracy to keep all its secrets is still terrible at keeping secrets.
“Hey, Dana Scully just ordered a bunch of DNA tests on a repeated abductee. Should we make sure they come back negative?”
“Nah, let’s make the abductee lie on camera, shut down the show she was working with after they talk about that having let it run for years, and then blow up her car with a fake UFO. Much more subtle.”
“So... we let Scully have the tests?”
“Huh? Oh. Whatever.”
Obviously this is partially for reasons of This Is A TV Show where Mulder and Scully can’t be completely blocked as soon as possible by a really watertight conspiracy. (See also The Omen, where a string of people die in mysterious ways immediately after passing on the knowledge needed to stop the Antichrist.)
Any secret organisation that protagonists go up against can’t stay entirely secret - the trick is not to make it look like they are in-setting except for their bungling around the heroes.
The X Files introduced a highly-placed informant in its first regular episode for this reason, and had factions fighting over its direction and in some cases looking after the investigators to explain the “why don’t you just shoot them?” issue as well. This does at times go too far, just as the conspiracy’s ultimate plan gets way too complicated for the sake of including new cool things - Bees! Oil! Huh?
I’ve done this myself - I know the appeal of the twist that you then have to explain.
Conspiracy-building advice in games like Night’s Black Agents includes ways in. There has to be a gap, or the story gets frustrating. Just don’t make it too obvious... unless it’s a trick...