Since its introduction in Strange Tales #135 (by Stan Lee, Jack Kirby, Dick Ayers, and Artie Simek), the international intelligence agency S.H.I.E.L.D, aka the Strategic Homeland Intervention, Enforcement, and Logistics Division, has played a pivotal role in the protection of the Marvel universe. However, while S.H.I.E.L.D has saved countless lives and served as one of the superhero community's greatest allies, the agency is far from perfect. Whether they are the direct result of the agency's overzealousness or the indirect results of a well-intended operation, S.H.I.E.L.D has been responsible for many high-profile incidents that have threatened the safety of the world they've sworn to protect.
Many of S.H.I.E.L.D's greatest failures can be directly linked to the agency's director, who holds absolute power over the organization. Over the years, many characters have served as the director of S.H.I.E.L.D, and even the best of them have made one or more terrible decisions that ended up putting the world in jeopardy. The ongoing Captain America/Iron Man series by Derek Landy and Angel Unzueta has shed a blunt and scathing light on S.H.I.E.L.D's legacy by raising the ghosts of both heroes' disastrous tenures as the agency's director and asking the very poignant question of whether or not the world is better off without the recently-disbanded organization.
When the Superhuman Registration Act was signed into law following the destruction of Stamford, Connecticut, Iron Man became its most outspoken supporter within the superhero community, ultimately leading the Pro-Registration movement to victory against the Anti-Registration resistance during Civil War. Following this success, the president of the United States appointed Iron Man as director of S.H.I.E.L.D, allowing him to establish the 50-State Initiative, which established a team of superheroes in every state. Unfortunately, Iron Man's faith in the Superhuman Registration Act soon turned into zealotry, and his persecution of the heroes who refused to follow it allowed the shape-shifting Skrulls to infiltrate S.H.I.E.L.D and instigate Secret Invasion. Completely disgraced by his inability to prevent the invasion, Iron Man lost his position to Norman Osborn, who promptly used the 5o-State Initiative to further his power and influence.
Following Osborn's downfall, Captain America stepped in to help rebuild S.H.I.E.L.D, but he wouldn't become its director until the end of Avengers: Standoff!. Following the discovery that then-director Maria Hill had been using a sentient Cosmic Cube named Kobik to brainwash villains into believing they were powerless residents of the small town of Pleasant Hills, the supposedly incorruptible Captain America was offered her position. However, the Red Skull had secretly manipulated Kobik into replacing the original Captain America with a fascistic doppelganger loyal to Hydra, who used his influence to transform the United States into a dictatorship during Secret Empire. Although the original Captain America eventually returned and overthrew his twisted counterpart, the crimes that "Hydra-Cap" committed deeply tainted his reputation.
Although many years have passed since they were removed from their position, Captain America/Iron Man shows that both heroes' actions as S.H.I.E.L.D directors are still putting people's lives in danger, with a resurgent Hydra finding a powerful recruit in Fifty-One, a former member of the 50-States Initiative. This situation is just one of the many times that the choices of a S.H.I.E.L.D director have had horrifying consequences. Nick Fury's unsanctioned invasion of Latveria during Secret War resulted in a brutal counter-invasion that devastated New York City, and Maria Hill committed countless human rights violations during the creation of Pleasant Hills. Even Daisy Johnson, who was chosen to lead S.H.I.E.L.D by Captain America, ultimately abused her authority by ordering the assassination of the Scientist Supreme.
Despite their best intentions, the various directors of S.H.I.E.L.D often caused more harm than good, and their failures serve as examples of the inherent flaws that have been present in S.H.I.E.L.D since it was founded. As an international law-enforcement agency, S.H.I.E.L.D was allowed to operate with little to no oversight, and its seemingly limitless resources gave the organization's leaders the power to do almost anything they wanted. Without having to answer to or interact with the people they're supposed to serve, it's only natural that S.H.I.E.L.D's leadership would become detached from the consequences that their actions may have. In fact, the organization's service to the "greater good" actively encouraged this sort of thinking.
Faced with the responsibility of protecting the entire world, even heroes like Captain America and Iron Man slipped into an "ends justify the means" mindset that blinded them to the subtler consequences of their decisions, and those little compromises eventually accumulated until they outweighed whatever good they accomplished.
Since its disbandment in the aftermath of Secret Empire, S.H.I.E.L.D has remained out of the picture within the Marvel universe, and that may ultimately be for the best. Despite its best intentions, S.H.I.E.L.D almost always ended up becoming the biggest threat to the safety of the world.