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Secret Invasion
While in hiding after the events of Secret War, Nick Fury uncovers evidence of the Secret Invasion. Realizing that he can't trust any of his former allies, he sends Daisy Johnson to gather a new team of "caterpillars"- young super humans whose existence is known to Fury alone. All of them accept, except Layla Miller. When the Skrulls invade New York, Nick Fury and the Secret Warriors arrive and rescue the defeated Young Avengers and Initiative members before withdrawing from the battle. The Warriors help the other heroes defeat the Skrulls, before teleporting to an unknown location.
Dark Reign
With Norman Osborn in complete control of H.A.M.M.E.R., the new organization replacing S.H.I.E.L.D., he declares to the team that "these are dark and desperate times". He also seeks to take out the remaining of the covert bases of S.H.I.E.L.D. still in existence.
Quake is leading the team in shutting down a covert base in Texas when HYDRA appears and attacks the team. As the Secret Warriors attempt to evacuate, H.A.M.M.E.R. surrounds the area, but they are able to escape. Nick Fury confronts the team on their failures, but specifically talks to Daisy about information he has uncovered. A month before, Fury infiltrated a covert Chicago base and downloaded for all information about the previous and current command structures of S.H.I.E.L.D.. A few weeks later, he confronts the new U.S. president about the deactivation of S.H.I.E.L.D. and gives him the location of two of the organization's covert bases. He reveals to Daisy that HYDRA was on a recovery mission at the Texas base, and that S.H.I.E.L.D. is a branch of HYDRA, while various agencies of the United States Government (NSA, Department of Treasury, FBI Science and Technology Branch), as well as the Canadian Security Intelligence Service and the Russian Main Intelligence Directorate and Foreign Intelligence Service are all under HYDRA control.
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