The second Captain America movie - Captain America: The Winter Soldier - saw the demise of S.H.I.E.L.D. Hydra - an evil organisation thought to have been long dead - had been secretly and parasitically infecting the espionage organisation for nearly seventy years and they succeeded in bringing it down. Rather appropriately, the third Captain America movie - Captain America: Civil War - should be the movie in which they truly reappear. Phil Coulson is currently putting the organisation back together, slowly but surely, in the Agents of S.H.I.E.L.D. television series. By the time Civil War comes around, they'll be a prominent advocate of the Superhuman Registration Act, as super-powered characters will likely be encouraged to work for them.