Fury becomes the second commander of S.H.I.E.L.D. as its Public Director. The ultimate authority of S.H.I.E.L.D. is revealed to be a cabal of 12 mysterious men and women who give Fury his orders and operational structure, leaving Fury to manage the actual implementation of these orders and strategems. The identities of these people have never been revealed; they appear only as shaded figures on monitors. Initially, his organization’s primary nemesis is the international terrorist organization Hydra, created by Fury’s worst enemy of World War II, Baron Wolfgang von Strucker (after retconning of the original continuity). Under Fury, S.H.I.E.L.D. grows into one of the world’s most powerful organizations, reaching covertly into national governments and forming strategic alliances with the Avengers and other superhero groups, while always maintaining independence and deniability. Fury soon becomes the superhero community’s main contact when government-related information is required in order to deal with a crisis.
After years at the helm, Fury discovers that S.H.I.E.L.D. and Hydra have both fallen under the control of a group of sentient Life Model Decoy androids known as Deltites. Betrayed, Fury goes to ground, hunted by his fellow agents, many of whom are later revealed to have been replaced with Deltites. Although Fury ultimately exposes and overcomes the Deltite threat, the conflict is so destructive to S.H.I.E.L.D.’s personnel and infrastructure, and leaves Fury so disillusioned, that he disbands the agency to prevent it from again being subverted from within.
Fury rebuilds S.H.I.E.L.D. from the ground up, initially as a more streamlined agency small enough for him to personally oversee and protect from being corrupted. This new incarnation changed the acronym to stand for “Strategic Hazard Intervention, Espionage and Logistics Directorate”.