The FBI will be on their own for the time being. But as the investigation develops links and ties might be made such as CIA to FBI or FBI to Ark corp. The objective is to gain CIA's full cooperation on the investigation.. The problem is that the FBI doesn't even know about what CIA knows. Only these two agents can create that link and therefore can be a major threat, even target for the fallen shadows.

So at the moment the FBI is not aware of Ark corporation's affiliation yet. I'd expect an alliance to form when the major discoveries (ontop of the ones already made) surface