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The feds were using the shotgun charge as leverage. Ultimately it is what he was charged with.

“In 1989, Weaver supplied two modified shotguns to Faderley. The ATF maintained that the weapons supplied by Weaver were illegally shortened 

Weaver was then approached by ATF agents and told that they had evidence of his possession and sale of illegal weapons, and offered to drop the charges in return for his co-operation in infiltrating the Aryan Nations. Weaver refused. He was initially arrested by ATF agents on charges[5] relating to transfer of a short-barreled shotgun without a license in January” Wikipedia