In the Marvel Universe, S.H.I.E.L.D. is often heralded as one of the premier intelligence agencies in the world. The big reveal at the end of 2008's Iron Man, which launched the Marvel Cinematic Universe incarnation of the agency, hinges on the organization adopting the familiar acronym as its preferred moniker.
Bridging together the early films of the shared cinematic universe, this version would star in the inaugural and longest-running MCU television series, Agents of S.H.I.E.L.D., with lingering rumors of a new series being developed directly by Marvel Studios for Disney+ surfacing late last year. Despite their popularity and visibility within the MCU, though, it has to be observed that, for such a seemingly elite organization that is regularly tasked with defending the fate of the free world and safeguarding its highly confidential secrets, the cinematic universe's incarnation of the venerable spy agency is terrible at its job.
Promotional materials for the MCU's next film, Captain Marvel, tease the agency's untold adventures from over 20 years ago as a younger Nick Fury and Phil Coulson begin their intelligence careers with the organization. Marvel Studios' special advance look at the film revealed that the extraterrestrial Skrulls have secretly invaded S.H.I.E.L.D., with the Skrull commander, Talos, seen disguised in his human form as an official above Fury's rank.
This infiltration marks at least the second time the highest levels of S.H.I.E.L.D. have been compromised, the first being the reveal that Hydra had successfully hid within the ranks of the fledgling organization after enlisting top scientists, including Doctor Arnim Zola, at the end of World War II. Under Zola's supervision, S.H.I.E.L.D.'s global agenda was secretly monitored and manipulated by Hydra sleeper agents for decades through assassination and keen politicking. That is, until Fury, Captain America and Black Widow uncovered the truth in Captain America: The Winter Soldier.
The full scope of Hydra's infiltration of S.H.I.E.L.D. would be explored throughout much of the first three seasons of Agents of S.H.I.E.L.D. as Coulson led his team to combat the unveiled terrorist organization, continually preventing their manipulation of the compromised spy agency. The fourth season of the ABC series saw a shift within S.H.I.E.L.D. as the agency was compromised by the malevolent artificial intelligence Aida, the program replacing agents with Life Model Decoys to further her own sinister agenda. For an agency entrusted with the world's greatest secrets and well-being, it seems to be chronically vulnerable to literally becoming its own worst enemy.
What makes the Skrull infiltration particularly problematic for S.H.I.E.L.D.'s already checkered reputation is that the '90s setting of Captain Marvel means that the covert alien invasion overlaps with Hydra's greater machinations, meaning the agency has been compromised by two hostile factions (at least) simultaneously. It's a wonder that Hydra and the Skrulls never became aware of each other during their respective plots. With their differing agendas, the Skrulls may not have felt threatened had they discovered Hydra's own devious plans within S.H.I.E.L.D.