As for the agents, S.H.I.E.L.D. will definitely have a visible presence, but it's going to endlessly annoy the FBI trying to do their job. Up until this point, S.H.I.E.L.D. has been glorified as a conspiracy theorist's wet dream, with the more street-wise FBI saying stuff like, "What, they called in S.H.I.E.L.D.? Oh great, aren't they those psychos always chasing UFOs and Bigfoot?" Since the world has been largely "normal" prior to the Terrigen Crisis, S.H.I.E.L.D. has not yet evolved into the enormous agency it is in canon. In this version, it stands for Special Hazard Investigation, Enforcement, & Logistics Division. They basically gather intel on anything deemed to be a "Special Hazard," dating back to the days of the SSR (Strategic Scientific Reserve) in the 1940s. The sudden emergence of over a hundred mutants is going to immensely expand S.H.I.E.L.D. and it's operations, with President Takei signing an Executive Order to triple the size of the agency to deal with the new influx of Special Hazards.