What are the bees
They are first used to spread the smallpox virus and when The Syndicate finds that successful, they plan to use it to spread The Black Oil...Purity...or, as I like to say so the scary, baby clawed aliens can then nest and gestate in your body.
Why the bees
First there's this:
"I don't believe the FBI currently has an investigative unit qualified to pursue the evidence in hand."
Where you can find the bees
The X-Files: Fight the Future
"War of the Coprophages"
If you want to know more about the bees click here.