This article contains spoilers for Captain America: The Winter Soldier.
There’s a world-shaking twist in Captain America: The Winter Soldier, and it rewrites everything we knew about the Marvel Cinematic Universe while also clearing the board to start Marvel Phase Three. It turns out that SHIELD - the big spy organization that has been keeping the peace in their flying Helicarrier under the single watchful eye of Nick Fury - has been totally compromised by evil terrorist organization Hydra. There’s no way of knowing just what percent of SHIELD was corrupt, but the problem reached all the way to the top, and in the end it was decided that SHIELD needed to be dismantled to deal with the Hydra infestation.
There’s been some confusion about just how and when Hydra infiltrated SHIELD; all of the pertinent information is given in the film, but some people seemed to have missed out on elements of the massive infodump, which included links to real world events in the wake of WWII. Without resorting to comic book knowledge I present to you the basic outline of it all:
SHIELD grew out of the Strategic Science Reserve, the secret program that made Steve Rogers Captain America. After WWII ended Howard Stark called Peggy Carter to Washington DC and together, along with Howling Commando Dum Dum Dugan, they founded the new super spy organization. This reflects reality - the Office of Strategic Services (OSS), the WWII spy group of the Allies, morphed into the Central Intelligence Agency after the war.
Just as a side note, the idea of Peggy Carter, a Brit, hanging out with the super science version of the OSS is historically accurate. The OSS had a secret Canadian facility called Camp X (they knew how to name this shit) where British Special Operatives trained OSS agents in ‘assassination and elimination’ tactics.
The forming of SHIELD closely mirrors the creation of the CIA. In 1946, the year of the Agent Carter Marvel One Shot, President Truman created the Central Intelligence Group which, in the National Security Act of 1947 would become the Central Intelligence Agency. In reality the splintered post-OSS spy groups, like the Strategic Services Unit, came together under the CIA, but we can see how in the MCU SHIELD stayed independent.
But what about Hydra? How could Arnim Zola have brought all of his Hydra buddies into SHIELD in the first place? Wasn’t anyone paying attention? The movie quickly explains this through the Black Widow - it was all accomplished through Operation Paperclip.
While other parts of SHIELD’s fictional history mirror reality, this borrows directly from it. Operation Paperclip was a real program, one that took Nazi scientists and brought them to America to work on sometimes secret projects. Using fake backgrounds, of course.
As WWII came to an end both the US and the Soviet Union raced into Germany. The Nazis had been making terrific scientific advancement, especially in rocketry, and the Allies did not want this expertise falling into the hands of the Russians. Even before WWII was officially finished the Cold War had begun, and the US knew the Russians would be the next great enemy.
Stage one of Paperclip was actually getting the scientists. The OSS was aided by the fact that the Germans, ever good with paperwork, had assembled their own list of intellectuals and thinkers. As the war on the Russian front had gone sour, Berlin recalled their scientists from the front lines in order to speed up research and development of new weapons. There was a list - the Osenberg List - that was discovered in a toilet where some dumb Nazi had attempted flush it away. The list got to MI6, who gave it to the OSS. As the Soviets advanced the American spies worked to find and detain as many scientists as they could. They did this in the excellently named Operation Overcast.
By 1947 the OSS had about 1800 scientists. They began putting them to work immediately - even as the war against Germany wound down the war in the Pacific raged on, and especially German work in infrared was seen as helpful against the Japanese. Part of the operation was also figuring out which scientists had worked with the Japanese Empire, and to figure out what sort of technology had made it into their hands.
Paperclip wasn’t official until August of 1945, but it was happening unofficially since the day Berlin fell. When Harry Truman did sign the order to make it 'real' there was a hiccup - his order expressly forbade recruiting anyone known "to have been a member of the Nazi Party, and more than a nominal participant in its activities, or an active supporter of Nazi militarism." This, of course, excluded just about every great scientist the OSS wanted. They had all worked on rocket programs and in concentration camps.
The solution was simple: lie. The spies created new biographies and political affiliations for the scientists and scrubbed away any records of their actual activities. Now seen as squeaky-clean, the scientists were allowed to enter the United States. Operation Paperclip got its name from the paperclips that attached these new, fake backgrounds to the official, real dossiers of the scientists.
Probably the most famous scientist to have come to America under Paperclip was Werner von Braun (shown in the picture above with other Paperclip scientists at Fort Bliss; he is popularly known as “the Father of Rocket Science,” and it was his expertise that allowed the United States to finally win the Space Race. von Braun ended up being such a staple of the US space program that he appeared on Walt’s Disney’s Disneyland show in an episode called Man In Space. That was 1955; just 11 years earlier von Braun had been personally choosing prisoners from Buchenwald to be slave labor for V2 rocket production. The V2 slaves were treated so badly that it’s estimated more people died MAKING V2 rockets than were killed by V2 rockets.
von Braun is the obvious analogue for Arnim Zola (and it's no mistake that Iron Man 2 makes Howard Stark something of a Walt Disney figure). This was a man who had worked with the Nazis to create their most fearsome weapons but who claimed to have very little personal affiliation with the regime itself. That lines up with Zola as shown in Captain America: The First Avenger - he was a guy very ready to flip on the Red Skull as soon as he was captured.
If Zola was captured in 1944 he was likely one of the first scientists secured through Paperclip; he would have already been working for the US by the time SHIELD was founded in 1946. It seems likely that Howard Stark already had Zola doing some work for him at SSR; when the new organization started up they probably brought Zola along. This means that Zola - secretly still loyal to Hydra - was there from day one. Which means the Hydra cancer was in SHIELD from the very first day it was founded.
I know I promised to not bring in the comics, but I must, as this was exactly what comic readers learned in the series Secret Warriors. After SHIELD is dismantled following an alien invasion (replaced by a group called HAMMER), Nick Fury learned that SHIELD had been infiltrated from the start and he gathers a team of new agents to help him battle not just HAMMER but also the remnants of Hydra. This wasn’t the first time SHIELD had been compromised, by the way - the organization had been taken over by android doubles known as Deltites before, leading to SHIELD’s first disbanding.
It's also worth noting that, in the comics, Hydra predates World War II. They actually predate the Marvel Comics Universe, first appearing in 1954, but in the fictional history they began sometime around the Third Dynasty of Egypt. They've been a secret criminal organization over the millenia, and would reappear around WWII as a part of The Hand, a ninja group famous for battling Daredevil. During the Second World War Baron von Strucker seized control of Hydra from the Japanese; he's been more or less leading the group since, thanks to all sorts of comic book-y resurrections and stuff.
In an article complaining about ten things that supposedly make no sense in the Marvel Cinematic Universe, an io9 writer wondered how stupid SHIELD would have to be to let Hydra get such a foothold in their organization. Just as stupid as the US government, since von Braun was only one of thousands of Nazi scientists who worked in the most sensitive and important areas of research and development after the war, including the White Sands Proving Grounds. And the new backgrounds of these scientists were air tight for years. How air tight? In 1977 Brooks Air Force Base in Texas named their library after Hubertus Strughold (what a Hydra name, huh?). They had to rename it a couple of years later when it came to light that Strughold had conducted medical experiments at Dachau that tortured and killed hundreds. The experiments were tests of ejection at high altitude, and some inmates had their brains dissected while alive. This could have been research that Strughold would have used to benefit the United States Air Force.