Nick Fury was working behind the scenes to bring his superhero team together long before the first Avengers movie. 2012's The Avengers finally realized that dream, but the the superhero team’s mission to save New York from alien invaders didn't get that much support from S.H.I.E.L.D. The government organization actually wanted to nuke the entire city, including the Avengers themselves.
It never really made sense, and a persuasive new fan theory could fix this glaring Avengers plot hole by using the subsequent movies to reveal SHIELD's true intentions.
During the Battle of New York, the Avengers were the only ones fighting the Chitauri and attempting to close their portal to Earth. Sure, Fury’s superiors in the World Security Council had approved some troops to assist the superhero team on the ground, but it wasn’t enough.
Considering the resources at their disposal, it’s safe to say that the agency did relatively little to help thwart the threat. Rather, the SHIELD council decided that Manhattan needed to be destroyed by a nuclear missile to contain the threat. In the moment, it sort of makes sense, but in hindsight, this feels like a terrible idea considering the damage a nuclear blast in the middle of Manhattan would do.
Isn't SHIELD supposed to protect people? What was their problem?
Reddit user u/elgarraz theorizes that Hydra — the Nazi organization that we learn in Captain America: The Winter Soldier has infiltrated SHIELD — was behind the decision to nuke Manhattan. Naturally, it was for nefarious reasons: Nuking NYC would have killed most of the Avengers — including Iron Man, whose funds and inventions advanced the team’s prominence and goals in future films — and likely disbanded the team for good.
“Eliminating Clint and Natasha would pave the way for Crossbones to take over as the top SHIELD agent. Plus, the nuke would eliminate several of the threats identified by Zola's algorithm in Winter Soldier, like Stephen Strange,” the theorist writes.
Whereas SHIELD would have gained nothing by nuking the city, Hydra could have used it to their advantage, leaving the world more vulnerable to a mass takeover ever earlier than expected. After all, Hydra was around for decades prior to SHIELD, so why not use a battle with aliens to further their own agenda?
What’s more, the theory also suggests that the push to blame the Avengers for the Chitauri invasion and subsequent damage to Manhattan was “engineered by Hydra” to weaken public support for the superheroes. This might all just be a clever retcon (did Marvel Studios even know Hydra would be a thing when The Avengers was filmed?), but it holds up to scrutiny and makes an MCU villain even more villainous.
This Avengers theory definitely makes sense in the grand scheme of the MCU, especially considering the many years that Hydra spent infiltrating SHIELD. Their overarching influence wasn’t revealed until Captain America: Civil War, but that rise to power clearly didn’t happen overnight.
The Avengers is currently available to stream on Disney+.