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In the third Captain America film, we see that the winter soldier is sent to assassinate Howard Stark and retrieve something that Hydra eventually uses to create the next group of winter soldiers. Since the winter soldier was given the mission, it means that Hydra couldn't create whatever it was that they were after. Since Howard's death takes place during/after his SHIELD days (we know he was part of SHIELD because it was shown in Ant Man), does this mean that SHIELD was starting up another super-soldier program? Or, was the substance just something new Howard came up with?

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    Coulson says (in The Avengers) that a lot of people were attempting to reproduce the serum that created Captain America. It stands to reason that SHIELD was. – Jack B Nimble Jun 1 '16 at 18:29
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One of the fundamental aspects to the Marvel Cinematic Universe is the running theme of developing metahuman capabilities.

  • After the discovery of the Tesseract (later revealed as the Space Stone) which was presumed to be an alien technology far beyond the reach of our own; secret government and private organizations (SHIELD and Hydra) decided to create such abilities and technologies on Earth from their attempts to reverse engineer it.

Such technology implied two things:

  • there were creatures out beyond our solar system whose technology eclipsed anything we have ever conceived of. Technology even with the Earth's best minds had barely scratched the surface of their potential.

  • These aliens used spaceships and have been to Earth at some point in the past. The greatest fear was their ultimate return and whether we would be a match for them when they arrived.

These two thought processes are behind much of the work SHIELD does in their attempt to recreate the super-soldier serum which produced the most effective operative the US military had ever known, Captain America. Since a great deal of the MCU seems based on the parts of the Ultimates timeline (Earth-1610), such an arms races behind the scenes is both reasonable and expected.

  • While it is conceivable we would use such operatives for our defense, it is also more likely it would just be used as another means of making war on Earth.

  • Given its date of origin, (in 1942) it seems inevitable that the formula could be recreated if given enough time, and it appears that late in Howard Stark's life, many decades later, he or a group of people who worked with him were successful in creating a variant of the serum.

  • But it is also implied the people who used it may have been driven insane by it thus it have been stolen before it could be vigorously tested.

Given the nature of spy vs spy operations, perhaps Stark was carrying the material simply because it was thought, given its value, he would be the last way anyone would think to transport it. But since we are now also aware, Hydra had operatives within SHIELD so they may have known what SHIELD knew and thus were able to get the substance despite SHIELD's probable bait and switch tactics.

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