With the collapse of the original incarnation of S.H.I.E.L.D., some members who were opposed to Hydra saw an opportunity to move away from Director Fury's 'cloak and dagger' remit and instil more transparency and accountability. These people did not rejoin Coulson's new "official" version, but instead struck out on their own, keeping their very existence a secret. Unlike the original S.H.I.E.L.D. that had one director with authority over all other agents, this version of S.H.I.E.L.D. had a more democratic style leadership with a board of directors that reached decisions based on majority rule.