The Strategic Homeland Intervention, Enforcement and Logistics Division, otherwise known as S.H.I.E.L.D., has always served as a protective barrier between the normal and extraordinary worlds. They mitigate mythical, mystical, and super-powered threats that most of us never even hear of. They operate under the radar and typically don't truly answer to anyone other than their director, Nick Fury.
Just because S.H.I.E.L.D. is supposed to protect the people, that doesn't mean they don't also put them in danger. Like their evil counterpart Hydra, S.H.I.E.L.D. has plenty of moments in which they do more harm than good, even if they don't realize it. With that being said, let's take a look at ten instances in which S.H.I.E.L.D. posed a bigger threat than the sinister Hydra.
10 Helicarriers
In both Marvel Comics and the MCU, the helicarrier is a symbolic defense force of S.H.I.E.L.D. The helicarriers have been around just as long as the organization, having been introduced way back in Strange Tales #135 by Jack Kirby back in 1965. Although these massive ship carriers fitted with an arsenal of weapons are meant to protect people from larger-than-life threats, they actually are much more threatening from the other side of the spectrum. We saw the terrifying possibilities of the helicarriers executed in Captain America: The Winter Soldier, and who's to say that couldn't happen at any point at the hands of S.H.I.E.L.D.?
9 Daisy Johnson
Much like the helicarriers, Daisy Johnson has typically been a staple of the S.H.I.E.L.D. organization. Especially since the inception of Marvel's Agents of S.H.I.E.L.D., people have come to associate Quake as a top agent.
Not to say that she isn't a fan favorite, but it's worth noting the potential threat that she causes. The earthquake-generating abilities that allow her to literally shake the Earth could potentially lead to a world-ending event in the absolute worst of circumstances. So, even though Daisy Johnson fights for the right side, it's the destruction her powers can cause that make her association with S.H.I.E.L.D. such a massive threat to the world.
8 Project Lazarus
In the history of both S.H.I.E.L.D. and Hydra, the process of human experimentation has been an extremely c0mmon element. From the S.H.I.E.L.D. side of the things, one of the first times the organization looked to enhance humans was in Defenders #126 in 1983 with Project Lazarus.
Project Lazarus, otherwise known as the Olympus Project, was a simple human-enhancement experiment that went horribly wrong. S.H.I.E.L.D. scientist Edward Cobert ended up testing the serum on himself, turning himself into a massive being with minimal intelligence labeled "Gargantuan". Project Lazarus showcased just how dangerous these S.H.I.E.L.D. experiments could become and how the very existence of them was a worldwide threat.
7 Weapon X Program
The Weapon X Program is yet another human-experimentation project that showcased the immense power that S.H.I.E.L.D. possessed through the form of superhumans. We mainly know Weapon X as the program that, in some Marvel universes such as the Ultimate universe, gave Wolverine his adamantium skeleton along with wiping his memory. Although the program ultimately was shut down, it still put S.H.I.E.L.D. in possession of god-like powers that could've seriously threatened the world around them.
6 Super Soldier Programs
Although the two above mentioned instances could fall under this category, it's best we give the use of super soldiers its own time to shine. Since the creation of Captain America, S.H.I.E.L.D. has been in the business of utilizing scientifically-enhanced soldiers in tactical, strategic, and combat missions.
Most of the time the organization had a grasp on the soldiers they were using. In other instances, that wasn't exactly the case. In either, however, the plan and more importantly the soldier could have easily backfired on them and posed a threat to the general public. Even though the thought behind using super soldiers to their advantage was a safe one, S.H.I.E.L.D. never seemed to consider the danger or damage that one of their soldiers could cause.
5 Agent Hulk
Speaking of genetically-enhanced soldiers with little control and the ability to cause massive danger and damage. Yes, that's right. At one point the famed scientist Bruce Banner, horrifically affected by gamma radiation to turn into the Hulk, was an agent of S.H.I.E.L.D.
As a deal that allowed Banner to utilize the organization's technology, facilities, and finances, S.H.I.E.L.D. was able to secure his powerful alter-ego as their most powerful agent. The Hulk essentially became a weapon of destruction for S.H.I.E.L.D., helping them take down their most powerful enemies with ease. What could possibly pose a threat more than letting the Hulk loose in the world with the intent of doing your bidding for you? It's undoubtedly something Hydra would conjure up.
4 LMD's
Life model decoys have always been a frequent issue in the Marvel Universe. Well, they also became a massive issue for S.H.I.E.L.D. at one point. During the 1998 Nick Fury vs. S.H.I.E.L.D. event from Bob Harras and Paul Neary, these androids became an Ultron-level threat to both the organization and the world.
When one of these decoys gained sentience and began a hostile takeover of S.H.I.E.L.D., it almost became too much to contain. Although Nick Fury was eventually successful in bringing this being down, it definitely threatened those both in and out of S.H.I.E.L.D. We've seen before the danger that a sentient robot (Ultron) can cause, and S.H.I.E.L.D. was nearly responsible for something like that happening once again.
3 H.A.M.M.E.R.
The events of Secret Invasion caused a massive change in the makeup of S.H.I.E.L.D. After being taken over by the villainous alien Skrulls, the organization was dissolved by the President and placed in control of who else but Norman Osborn.
Osborn turned S.H.I.E.L.D. into a sinister organization titled H.A.M.M.E.R., whose sole purpose was complete and dangerous domination. It became a home base of sorts for supervillains and brought the old S.H.I.E.L.D. down with it. Although it technically wasn't the work of S.H.I.E.L.D. performing these villainous deeds, it was the foundation of the old organization that made things so easy for Norman Osborn.
2 Secret Invasion
The question of, "What could've happened to Hydra if they were taken over by Skrulls?" is not one that can really be answered. However, it's easy to note what happened to S.H.I.E.L.D. in the same event. As a result of the hostile alien takeover, S.H.I.E.L.D. was obviously compromised and provided the Skrulls with a vast network of both heroes, spies, and agents to complete their invasion. Although it wasn't the direct fault of S.H.I.E.L.D., their manipulation and intervention with out-of-this-world belongings and beings definitely could've played a role in the buildup to the events of Secret Invasion.
1 Pleasant Hill
As a global peacekeeping organization responsible for some of the most powerful beings on this planet and others, S.H.I.E.L.D. is typically responsible for the capture and imprisonment of supervillains. Finally revealed in Nick Spencer's Avengers: Standoff, Maria Hill and S.H.I.E.L.D. concocted a prison unlike any other. "Pleasant Hill" was born using the cosmic cube Kobik and kept these villains at bay by altering their minds to make them believe they were well-mannered citizens of this fictional community.
Although it seemed like a great idea, "Pleasant Hill" ultimately backfired on S.H.I.E.L.D. and ended up becoming a massive threat to the outside world. The prisoners managed to escape and use the cosmic cube to bend reality, and thus Secret Empire was upon us. After seeing how the resulting events of Pleasant Hill drastically changed the world, it's safe to say that S.H.I.E.L.D.'s imagined prison community is up there with the worst things that Hydra ever pulled off.