A lot of us are probably wishing we could live inside the Marvel Cinematic Universe right now. But as much as we might yearn for a world where global threats (even as severe as invading extraterrestrial monsters or sassy killer robots) are promptly quelled by righteous superheroes, sadly it's not real. There's no such thing as a fusion "arc reactor" and gamma radiation wouldn't create The Hulk, it would simply create the limp corpse of Dr. Bruce Banner. Plus after twenty-three movies, multiple television shows, tie-in comics and a line of colognes that presumably smell like falafel and sweaty rubber, the MCU has made a few continuity errors. We've thought of one that, at first glance may seem like a sloppy plot-hole, but if you dig a little deeper, could be interpreted as a depressingly realistic in-universe screw-up.
At the beginning of 2012's The Avengers, we see that S.H.I.E.L.D. has been working on something called Project PEGASUS -- which sounds like a pre-teen prog rock band, and is also the name of the 1970s DARPA program that teleported a teenaged Barack Obama to Mars (according to a conspiracy theory that we can only assume Marvel and the Walt Disney Corporation believe to be 100% true). Headed by Dr. Erik Selvig, the project involves tinkering with the Tesseract, that glowy blue cube that holds the Space Stone. Things are not going well; Selvig's team can't figure out how to "harness" its energy.
Later Tony Stark and Bruce Banner discover that "Phase 2" of S.H.I.E.L.D 's plan is to use "the cube to make weapons."
We know this is possible because it's a major plot point in Captain America: The First Avenger. Johann Schmidt (AKA The Red Skull) steals the Tesseract and enlists Dr. Arnim Zola to experiment with its power. Within a fairly short span of time, Zola figures out how to build HYDRA's first Tesseract-powered weapon.
So by the time of The Avengers, Nick Fury and company are basically trying to invent a technology that already existed in 1943. That's like if all of S.H.I.E.L.D.'s immense resources were diligently working to create a color TV set. And it's not like they didn't have ample time to tinker with the Tesseract, Howard Stark recovered the cube in the '40s, and as we saw in Endgame, in 1970 it was just sitting around S.H.I.E.L.D. headquarters, as useful as a lava lamp, or a pet rock.
Even forgiving that Dr. Selvig and his team aren't able to accomplish what one lone Nazi scientist was able to, there's one big problem with this narrative; in Captain America: The Winter Soldier we learn that S.H.I.E.L.D. was infiltrated by Hydra following the war. So, how exactly could S.H.I.E.L.D. not replicate what HYDRA had already done when they were secretly run by HYDRA? That's like if a Burger King was full of McDonald's employees, but they still couldn't figure out how to make Big Mac sauce, even though it's obviously just mayonnaise, relish, and clown tears.
Project PEGASUS wasn't purely Nick Fury's endeavour, he reluctantly took the assignment given to him by the mysterious World Security Council, the shadowy cabal who oversee S.H.I.E.L.D. We know this because it was in the Avengers Prelude: Fury's Big Week tie-in comic that we're all obviously intimately acquainted with. The comic also reveals that the only reason Fury tasked Hawkeye with guarding Project PEGASUS was apparently because he was worried Black Widow would go man-crazy in a bunker full of horny dudes.
While the World Security Council don't know about the HYDRA takeover of S.H.I.E.L.D., they very possibly do know that, as we saw in The Winter Soldier, Dr. Zola's consciousness has been downloaded onto an old-timey computer.
So S.H.I.E.L.D. not only had the cube itself, but also access to the guy who successfully exploited its weapons potential. Yes he looks like a Commodore 64 game now, but he probably could have helped with S.H.I.E.L.D.'s attempts to replicate the thing he'd already done back when Louis Armstrong was still alive.
Somehow S.H.I.E.L.D. figured out how to cheat death using a computer less powerful than an iPhone 6, but they still can't crack how to utilize the Tesseract even with the help of Zola's cyberghost? And HYDRA's plan seems shockingly bad in retrospect; spending decades fomenting political unrest until humanity is willing to sacrifice their own freedoms is dastardly to be sure, but they already had access to a goddamn Infinity Stone and the technology to weaponize it. Why didn't they make a move prior to the 21st century? Instead of sneaking around for decades, why not just build a giant Tesseract-powered death ray in, like, the '70s?
Sure, we could just chalk this up to a minor storytelling hiccup, and move on with our lives -- but perhaps there's an answer that makes total sense within the world of the story. Could it not be that all of this is due purely to incompetence, pure and simple? That S.H.I.E.L.D/HYDRA grew into a bloated organization, bogged down in their own bureaucratic inertia and incapable of getting anything done? Anyone who's ever worked for a large company knows that even the simplest projects are likely to be delayed, stalled, and outright abandoned thanks to gross mismanagement. This might be the most relatable part of the entire Marvel Universe.
Just because they have superpowered friends, doesn't mean that S.H.I.E.L.D. and HYDRA wouldn't necessarily fall prey to the same systemic failings that other large-scale government operations do. Even our real-world law enforcement agencies have had some comically absurd failings over the years. The CIA once accidentally left a bunch of real explosives underneath an actual schoolbus for two whole days. A college student was once placed on a no-fly list by the FBI because an agent "checked the wrong boxes" on a form. To expect that S.H.I.E.L.D. wouldn't fall prey to the institutional failings of any large-scale enterprise is harder to believe than a giant purple alien who murders people with magic jewelry.
Top Image: Marvel Studios